Background and aims Tropical montane rainforests play an important role in increasing atmospheric N2O concentration. Although accurate estimations of N2O fluxes in tropical montane rainforests are critical for predicting global climate change, there are still considerable uncertainties about the spatial and temporal variability of the emissions. This study aims to investigate the effects of canopy gap caused by typhoons on N2O emissions, a key factor for understanding the spatial heterogeneity and supporting environmental regulations. Methods N2O fluxes were measured monthly using static chambers both inside and outside two large canopy gaps in the tropical montane rainforest of the Jianfengling National Natural Reserve on Hainan Island, south of China, from August 2012 to July 2013. Results Mean annual N2O emissions were 2.19 ± 0.43 kg N2O-N ha-1 yr-1 inside canopy gaps, and 1.19 ± 0.29 kg N2O-N ha-1 yr-1 outside canopy gaps, revealing substantial differences in N2O emissions resulting from forest structure. Moreover, N2O emission rates within canopy gaps during the wet season (2.89 kg N2O-N ha-1 yr-1) were significantly higher than those during the dry season (1.34 kg N2O-N ha-1 yr-1), suggesting strong regulation of soil moisture and precipitation in controlling soil N dynamics. However, there were significant nonlinear relationships between N2O fluxes and water filled pore space, and soil temperature within canopy gaps, but no significant relationships were found under the closed canopy. Conclusions Contribution of canopy gaps should be considered to avoid underestimation of N2O emission rates from disturbed forests. Interestingly, emissions from gaps are more strongly coupled with climate drivers (moisture and temperature), with important implications for climate change projections. Therefore, the further research is needed to study the biogeochemical processes and mechanisms behind such phenomenon.