To quantify the ratio of CH4 ebullition to total flux in subtropical shallow ponds, the CH4 flux at the water-air interface was measured using the inverted-funnel and water equilibrium methods in two small ponds in Quanjiao, Anhui Province from July 28 to August 13, 2016. The average CH4 ebullition fluxes were 121.78 and 161.08 mg·(m2·d)-1 and the average diffusion fluxes were 3.38 and 3.79 mg·(m2·d)-1 over pond A and pond B, respectively. The ebullition flux accounted for 97.5% and 96.4% of the total flux over pond A and pond B, respectively. Methane ebullition ranged from 0.11 to 446.90 mg·(m2·d)-1 over pond A and from 0.05 to 607.51 mg·(m2·d)-1 over pond B. Gas ebullition rate during the day was higher than that at night and was controlled by wind speed. Methane ebullition flux was influenced by wind speed over the shallow pond at hourly scale and by water depth and wind speed at daily scale, with positive correlation with wind speed and negative correlation with water depth. Varying with latitude, methane ebullition flux was higher for the water bodies in the mid-latitude region compared to those in the high-latitude region. Direct observations of the methane ebullition flux over small ponds provide data support and theoretical reference to precisely estimate the contribution of inland water bodies to regional and global carbon cycle.