The emission factor method (Tier 1) recommended by the Intergovernmental Panel on Climate Change (IPCC) is commonly used to estimate greenhouse gas (GHG) emissions from livestock and poultry farms. However, the estimation accuracy may vary due to practical differences in manure management across China. The objectives of this study were to estimate the direct and indirect nitrous oxide (N2O) emissions from dairy manure management between 1990 and 2021 in China and characterize its spatial and temporal variations following IPCC guideline Tier 2. The N2O emission factor (EF) of dairy cow manure management systems was determined at the national level and regional level as well. The results showed that the national cumulative N2O emission of manure management from 1990 to 2021 was 113.1million tons of CO2 equivalent, ranging from 90.3 to 135.9 million tons with an uncertainty of ±20.2%. The annual EF was 0.021 kg N2O-N (kg N)−1 for total emissions, while it was 0.014 kg N2O-N (kg N)−1 for direct emissions. The proportions of N2O emissions in North China, Northeast China, East China, Central and Southern China, Southwest China and Northwest China were 32.3%, 18.6%, 11.4%, 5.8%, 6.1% and 25.8%, respectively. In addition, N2O emissions varied among farms in different scales. The respective proportions of total N2O emissions from small-scale and large-scale farms were 64.8% and 35.2% in the past three decades. With the improvement in farm management and milk production efficiency, the N2O emissions per unit mass of milk decreased from 0.77 × 10−3 kg to 0.48 × 10−3 kg in 1990–2021. This study may provide important insights into compiling a GHG emission inventory and developing GHG emission reduction strategies for the dairy farming system in China.