I know how to solve this issue now.
Solution 1:
From the information of Is units different between engine and editor?, the model’s unit is incorrect. Regenerate the model json file, and make sure its unit is meter.
Solution 2:
It seems there is a limitation of the range of nearClip and farClip. In my case, 0.01 ~ 100000 is too large, so adjust them will work. I’ve tested on 100 ~ 100000, it works fine. See http://jsbin.com/husoxas/25/edit?js,output.