I found once the c++ include paths is modified, the problem will happen. So there maybe something wrong with the .cproject file within the proj.android folder.
Yes. Open the .cproject file and you will see there are 2 <cconfiguration> sections. When editing the c++ include paths in eclipse, only one of them is modified. This inconsistence cause the cdt crash.
Solution:
In fact there should only be one <cconfiguration>, so delete the second one, it start from line 85. After that you can edit c++ include paths in eclipse and no crash will happen.
ps:
Why should I edit the c++ include path of a newly created project? Because one of them is wrong:
${ProjDirPath}/…/cocos2d/cocos/math/kazmath, this path should be changed to ${ProjDirPath}/…/cocos2d/cocos/math