This study focuses on 19 provinces in the Yangtze River Basin of China. It gathers relevant data indicators from 2010 to 2021 and constructs an evaluation index system centered on agricultural science and technology innovation. The study evaluates the relationship between agricultural “science and technology innovation-economy-ecology” systems and identifies key obstacle factors using the obstacle degree model. The study draws the following conclusions: Firstly, the comprehensive development level index of the agricultural science and technology innovation system shows an overall linear upward trend (values range from 0.121 to 0.382). Secondly, the comprehensive development level index of the agricultural economic system exhibits an upward trend but with a relatively small overall magnitude (values range from 0.248 to 0.322). Thirdly, the comprehensive development level index of the agricultural ecological system demonstrates significant overall fluctuations, with notable regional disparities (values range from 0.384 to 0.414). Fourthly, the overall agricultural SEE (Science and technological innovation, Economy, Ecology) complex system exhibits a characteristic of “high coupling, low coordination”, identifying the main obstacle factors influencing agricultural SEECS based on a formulated approach. Subsequently, the following policy recommendations are proposed: Firstly, enhance the agricultural technological innovation system and promote green and efficient agricultural technology research and development. Secondly, to accelerate the transformation and upgrading of modern agriculture, achieving green and high-quality development of the agricultural economy. Thirdly, to strengthen agricultural ecological environment protection, laying a solid foundation for the healthy and sustainable development of agriculture.