Abstract: The research on the indirect value of rice production mainly focuses on ecosystem service functions, while there is little research on externalities. Evaluating the negative externalities of rice production can help promote agricultural ecological prevention and control and ecological civilization strategies. This article is based on panel data from prefecture level cities in Hunan Province from 2000 to 2021. Using methods such as market value method, standard deviation ellipse, trend surface analysis, geographic detector, and OLS regression, the negative externality value of rice production is calculated from six aspects including greenhouse gas emissions, and its spatiotemporal evolution characteristics are analyzed. At the same time, the impact of various natural and socio-economic factors on the negative externality value of rice production is explored. The results showed that: (1) The average annual negative externality value of rice production in Hunan Province from 2000 to 2021 was 24.663 billion yuan, and the negative externality value was mainly composed of greenhouse gas emissions (45.95%) and fertilizer pollution (21.04%). (2) From 2000 to 2014, the overall negative externality value of rice production in Hunan Province showed a slow upward trend. After reaching its peak in 2014, the growth trend was controlled and showed a slight fluctuation downward trend, reflecting the effectiveness of agricultural ecological protection in the new era. (3) The negative externality value exhibits significant spatial heterogeneity, with a higher concentration in the central and eastern regions of Hunan Province. The spatial distribution is characterized by higher values in the central and eastern regions and lower values in the western regions. The density of negative externality value is uneven across regions, and the overall spatial distribution is relatively stable over time without significant migration. (4) The negative externality value of rice production is influenced by the coupling of natural and socio-economic factors, and the interaction of these factors enhances its explanatory power. Negative externalities are significantly negatively correlated with average slope and total retail sales of consumer goods. Negative externalities are significantly positively correlated with precipitation resources, average elevation, regional GDP, rural population, disposable income of rural residents, and total power of agricultural machinery. The article innovatively analyzes the negative externalities of rice production in Hunan Province from a specific research object and dynamic spatial perspective, and puts forward specific suggestions for strengthening agricultural ecological protection and controlling the negative externalities of rice production from the aspects of government guidance, market guidance, farmer participation, and technological support.