Traditionally, nitrification inhibitor is applied together with basal fertilizer before transplanting or seeding of rice. A pot experiment in greenhouse was carried out to study effect of timing of application of nitrification inhibitor (dicyandiamide, DCD) on methane (CH4) and nitrous oxide (N2O) emissions during the rice growth period. Four treatments in triplicate including CK (without DCD), Treatment EA (early application of DCD together with basal fertilizer); Treatment DA (delayed application, 10 days after the top dressing at the tillering stage), and Treatment LA (late application, 10 days after the side-dressing), were implemented in this experiment. Results indicated that application of DCD inhibited both CH4 and N2O emissions, which was reduced by 21.41% and 8.00%, respectively in Treatment EA, by 30.30% and 5.24% in Treatment DA, and by 32.65% and 11.18% during the period from application of DCD to harvest of the crop in Treatment DA, but not much affected in Treatment LA. The CH4 flux in Treatments CK, EA, DA and LA was 0.95, 0.75, 0.87 and 0.94 mg/(m2·h), and N2O flux was 155.67, 143.24, 108.50 and 153.24 μg/(m2·h), respectively. Delayed application of DCD decreased CH4 and N2O emissions significantly (p＜0.01). Significant negative correlation between CH4 flux and soil Eh was observed and the fact that soil temperature was the main factor affecting N2O emission during the rice growth period was found.