Nitrogen-fixing cyanobacteria (NFC) play an important role in maintaining the N pool of paddy fields, but few studies have been conducted on the N fate of NFC, especially during the vegetative growth period of rice. Revealing the fate of N from NFC (NFC-N) is of great significance for the application of NFC in rice fields. A pot experiment with N-15-labeled NFC was carried out to determine the N-15 contents in rice plants and soil under different NFC application patterns. Four treatments were set up in the experiment: 1) CK: no N-15-labeled NFC applied; 2) C5: half application of N-15-labeled fresh NFC = 7.5 g NFC pot(-1); 3) C10: full application of N-15-labeled fresh NFC = 15 g NFC pot(-1); 4) HC10: full application of high temperature inactivated N-15-labeled NFC = 15 g NFC pot(-1). The results showed that NFC-N was detected in the roots, stems, and leaves of rice in the C5, C10 and HC10 treatments, but the amount of NFC-N absorbed by rice plants in these treatments was much less than the total N accumulated in the rice plants (including N absorbed from soil and irrigation water, etc.) during the vegetative growth period. Soil nutrients were mainly retained in topsoil due to the slow-release effect of NFC, accounting for 57-71% of the NFC-N application. A total of 17-32% of NFC-N was lost from the rice pot system, and the loss of NFC-N in the HC10 treatment was significantly higher than that in the C10 treatment. Therefore, this study suggested that NFC as biofertilizer should be combined with chemical N fertilizer to achieve a more optimized management effect of nitrogen fertilizers. Fresh NFC should be applied when conditions permit, which would be more beneficial to improve soil nutrient contents.