At first, I thought it was because of the new UI design was too bright (not clear) and the font did not look clear so I tried to calibrate the display to make it darker and increase contrast in Accessibility. Everything was better. It was clearer and easier to see. However, the problem still existed. I even copied the Display profile (*.icc files) from OS X Lion and used it on those new OSXs but no luck.
I gave up and sticked to OS X Mavericks for a while. Note that OS X Mavericks and priors are fine. In the beginning of September 2017, I started to learn Swift 4. As Swift 4 is compatible only with OS X 10.10 and laters, I tried to make research on this problem again. I went through several forums and someone said she had the same problem but her eyes seemed to be better when she changed the Display profile to "sRGB IEC61966-2.1". She said she couldn't see the difference when switching to that profile, but she felt better with switching to that profile. I tried it too but it didn't work.
After that, I tried the Apple RGB profile, which I copied from Windows 8 I installed on my MacBook Pro 13'', and my eye condition seemed to be 90% better. No pain in the eyes anymore. I could star at the screen for hours. Note that the other display profiles from Windows 8 didn't solve my problem. However, I still felt a little bit fatigue and got a little bit headache though.
To improve the fatigue eye condition, I then changed the Color Temperature in Night Shift setting to warmer may be at 40%. The headache issue resulted from small system font size. I increased it by decreasing the screen resolution from 1366x768 to 1280x720.
Overall, switching the Display profile, increasing the Color Temperature, and increasing system font size did improve my eye condition about 90% after I've tested it for a few hours. After using it for a few days, I feel my condition has 99% improved. I think my eyes is getting used to it.
Update 1
Today is 27th August 2021. I haven't used my MacBook Air 11'' (2013) for about a year, and today I started using it again. There are two versions of macOS, Mavericks and Sierra. At first, I tried Sierra and my eye hurt badly after staring at the screen just about 15 minutes. This means the fix I claimed to work above is no longer true. I don't know why. Then, I switched to Mavericks, and there was no pain in the eyes but i got eye strain, which made me hard to stare at the screen for even half an hour. It's odd. I can't use my MacBook Air anymore.
I did some research and some people said they got eyestrain and felt nausea with some new models of MacBook, and the cause is that the temporal dithering is enabled by default for recent versions of macOS. I don't know about the temporal dithering and whether it's the culprit. But, someone said macOS Big Sur has it disabled by default so I tried it, and my eye problem had gone though I still got mild eye strain.
However, it's unbearable getting mild eyestrain when I need to stare at the screen for a long time so I played with the Color Profiles.
The default color profile is Color LCD. First, I switched to another one, Color LCD, which is copied from my MacBook Pro running OS X Mountain Lion. My condition was a little bit better but I felt dizzy sometimes. Second, I tried sRGB IEC61966-2.1, and the dizziness was gone but the mild eyestrain was still there. Third, I switched to Generic RGB Profile, and I felt much better, almost no eyestrain and dizziness. It's still a bit uncomfortable looking at the screen for a long time, yet it's acceptable. Additionally, I turned on the Night Shift to reduce blue light, which was claimed by many on the net to cause eye strain, as following:
Fourth, I tried another profile color I copied from my MacBook Air running OS X Mavericks, and it felt more comfortable than Generic RGB Profile when staring at the screen long. However, I felt my eyes were so dry. Then, I turned off Night Shift (so the screen became a bit more blue), and it seemed to solve this problem. This is the best solution so far.
Update 2
According to this post, a calibrated profile on macOS implicitly disabled the dithering so I tried it. And IT WORKED, no eyestrain nor pain any more. It's been days already (I tested on macOS Sierra, High Sierra, and Big Sur).
Below is the color profile I calibrated. I first selected on Color LCD (a built-in profile) then clicked on Calibrate... button, and I did it with just a few clicks because I went for default options. I couldn't see the difference between the calibrated profile and the built-in one, and I didn't care as long as it worked.
Also, make sure to uncheck these options Reduce motion, Reduce transparency, Differentiate without color, and Increase contrast in Accessibility because my eyes felt uncomfortable when they were enabled. I didn't spend much time on testing it but unchecking them definitely caused no harm to my eyes.
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