At present, e-commerce mode has been gradually applied to agricultural science and technology production, which has played an important role in agricultural economic growth and production efficiency. At the same time, the fundamental way out for sustainable and stable development of agriculture is science and technology. Generally speaking, part of the growth of the agricultural economy comes from agricultural production factors. The increase in input is partly due to the improvement of productivity of agricultural elements. Therefore, based on the background of the e-commerce environment, this paper chooses the entropy method to study the relationship between agricultural science and technology input and agricultural economic growth. Compared with the exponential method and the Bolat method, the entropy method can scientifically determine the specific weight of the indicators based on the variation of each quantitative index, so as to improve the accuracy and objectivity of the quantitative index analysis and avoid the adverse effects of human factors. The entropy method is used to evaluate and analyze the development level of agricultural e-commerce, which improves the accuracy and reliability of the evaluation results. Based on this, this paper makes an empirical study on the relationship between agricultural science and technology input and agricultural economic growth by using the method of entropy under the mode of e-commerce, constructs the index system of agricultural productivity, evaluates the situation of agricultural science and technology input and agricultural economic growth, and studies the relationship between them by using the method of regression analysis. Research shows that the application of agricultural science and technology investment and e-commerce mode can promote agricultural economic growth.