Several models have been developed over the past decade to estimate CH4 emission from rice paddies. However, few models have been validated against field measurements with various parameters of soil, climate and agricultural practice. Thus reliability of the model's performance remains questionable particularly when extrapolating the model from site microscale to regional scale. In this paper, modification to the original model focuses on the effect of water regime on CH4 production/emission and the CH4 transport via bubbles. The modified model, named as CH4MOD, was then validated against a total of 94 field observations. These observations covered main rice cultivation regions from northern (Beijing, 40°30′N, 116°25′E) to southern China (Guangzhou, 23°08′N, 113°20′E), and from eastern (Hangzhou, 30°19′N, 120°12′E) to southwestern (Tuzu, 29°40′N, 103°50′E) China. Both single rice and double rice cultivations are distributed in these regions with different irrigation patterns and various types of organic matter incorporation. The observed seasonal amount of CH4 emission ranged from 3.1 to 761.7 kg C ha−1 with an average of 199.4 ± 187.3 kg C ha−1. In consonance with the observations, model simulations resulted in an average value of 224.6 ± 187.0 kg C ha−1, ranging from 13.9 to 824.3 kg C ha−1. Comparison between the computed and the observed seasonal CH4 emission yielded a correlation coefficient r2 of 0.84 with a slope of 0.92 and an intercept of 41.1 (n = 94, p < 0.001). It was concluded that the CH4MOD can reasonably simulate CH4 emissions from irrigated rice fields with a minimal number of inputs and parameters.