Emissions of non-carbon dioxide greenhouse gases (non-CO₂ GHGs), primarily methane (CH₄) and nitrous oxide (N₂O), are critical drivers of climate change, with China’s wastewater treatment sector ranking as the fourth-largest source of both gases. Consequently, establishing high–spatiotemporal-resolution inventories for CH₄ and N₂O emissions from this sector is a prerequisite for China to achieve its non-CO₂ GHG mitigation targets. This study develops a 0.1° × 0.1° spatial-resolution inventory for CH₄ and N₂O emissions from Chinese wastewater treatment plants (WWTPs) spanning 2000–2024. By integrating top-down and bottom-up methodologies, the inventory is used to establish a refined emission-factor database that distinguishes between technical processes and wastewater types. The results indicate that non-CO₂ GHG emissions of China’s WWTPs generally increased until 2015, followed by a steady decline through 2024. Emission hotspots have expanded from eastern to central China, with the top 10% of WWTPs accounting for around 60% of total emissions. These datasets provide a scientific basis for designing region-specific emission-mitigation policies.