The characteristic and experience of organizational change of the National Science Foundation (NSF) of US are briefly reviewed, and is compared with that of the National Natuar Science Foundation of China (NSFC). According to the requirement from the national innovation system and long-term planning of NSFC, the difference of supporting module design is compared between NSFC and some other scientific foundations. Finally, some suggestions about how to push forward organizational change in the future for the NSFC are put forward.