A Backward trajectory inversion model was established for estimating methane emission over Beijing area, with in situ data of methane measurement. The model was systematically tested for its ability on reflecting diffusion processes in atmospheric boundary layers. In specific condition, the model acted excellently on calculating emission strength and distribution over an area of 100 km scale. By applying to Beijing area with 9 days real methane data and practice meteorological data, the model showed source patches in this area with emission rate 0.0066-0.026 mg/(m2.s), which was correspond well to rice fields emission, the major methane source, in this region. Model results of source patches also showed certain spatial correlation with rice fields distribution.