Scholars have begun to systematically reflect on economic theories from the perspective of resilience. The emergence of the social-ecological system (SES) theory has had a significant impact on economic thought. Agricultural production, as a typical SES, requires the application of resilience thinking. Theoretically, this paper is based on the SES theory. It defines the basic functions of agricultural production and conducts a qualitative analysis and extension of the multi-dimensional resilience of the agricultural production system. Empirically, this paper combines databases such as FAO and the China Agricultural Statistical Yearbook. It employs a combination of locally weighted regression scatter smoothing, Shannon entropy methods, and generalized moment estimation methods to provide measurement indicators for analyzing the comprehensive resilience and multi-dimensional resilience of agricultural production. The theoretical analysis shows that the academic community should pay great attention to the complexity of agricultural resilience and re-examine and depict the resilience of the agricultural production system. The empirical results show that the comprehensive agricultural resilience in China exhibited a "W"-shaped evolution trend from 1990 to 2020, with the lowest values occurring in 2004 and 2016, respectively, and a rapid upward trend after 2016. The fluctuation resilience of grain production was relatively stable before 2016 without a clear trend, but it showed a rapid increase after that year. The ecological resilience showed an inverted "V" shape overall, with a significant downward trend after 2003. During the period from 2001 to 2019, the development resilience of China's agriculture exhibited an "N"-shaped upward trend, with Shanghai, Beijing, Tianjin, Guangdong, Zhejiang, and Liaoning showing more significant increases. The coupling coordination degree of the three types of resilience has been stable since 2004 and has been significantly improved after 2016, reflecting the further optimization and improvement of the relationship between the various dimensions of agricultural production resilience. For the first time, this paper constructs a multi-dimensional resilience indicator for agricultural production from the aspects of production, ecology, and development, providing a theoretical basis and analytical tool for a comprehensive understanding of agricultural resilience. Furthermore, this paper quantitatively measures the various dimensions of agricultural production resilience, more accurately reflecting the complexity and multi-dimensionality of the agricultural system and offering new ideas for the measurement of agricultural resilience. This paper also reveals the coupling coordination relationship between different dimensions of resilience, providing a theoretical basis and practical guidance for formulating agricultural support policies and enhancing the resilience of the agricultural production system.