In order to effectively guide the formulation of agricultural greenhouse gas emission reduction policies, CH4MOD model and emission factor method were used to estimate the emissions of methane (CH4) and nitrous oxide (N2O) from crops in the Yangtze River Delta (YRD) in 2018, and their temporal and spatial distribution were further analyzed, Finally, 1km × 1km grid greenhouse gas emission inventory of crops in the Yangtze River Delta in 2018 was established. The results showed that, the CH4 emission factor of paddy field in the YRD was 348.54 kg/hm2 and the nitrous oxide (N2O) emission factor of crops was 0.95 kg/hm2, which were consistent with previous research results. In 2018, 1.769 million tons of CH4 were discharged from paddy fields in the YRD (equivalent to 37.149 million tons of CO2), mainly from the Single-season paddy fields. 15114.9 tons of N2O were discharged from crops in the YRD in 2018 (equivalent to 4.504 million tons of CO2), and wheat was the largest contributor. The CH4 and N2O emissions were mainly originated from Jiangsu and Anhui provinces, especially from April to August. It is suggested to strengthen the control of agricultural greenhouse gas emissions and reduce the input of farmland carbon and nitrogen from the source.