The solution is create multiple source folder for your eclipse project.
1. In the project properties window, click "Java Build Path" node
2. Click "Source" tab
3. Click "Add folder..." button
4. Click "Create New Folder..." in the popup window
5. Input the folder name (such as "junit"), click "Finish" button
After that, the class files, which is generated from java file in "junit" folder, are saved in the "bin" folder. (like src folder java file)