To analyze the failure reasons for application of Natural Science Foundation of China (NSFC) and discuss their roles in improving the gain rate. By the retrospective method the failure reasons for natural nature science foundation were analyzed in Beijing Neurosurgery Institute from 2004 to 2008, and set up corresponding measures. Through summarizing the feed back opinions of 45 of application failure pro-jects it was found that the failures were dealt with insufficient of reliability, basis for argumentation , objec-tive ambiguous, personnel allocation unreseasonable and no time guarantee for project pedormance. A higher gain rate could be achieved by analyzing the failure reasons and making corresponding countermeasures.