High-quality development of agriculture is an inevitable requirement for China to advance from a large agricultural country to a strong agricultural country, and it is a proper meaning of high-quality development of China’s economy. Based on the panel data samples of 30 provinces (except Xizang, Hong Kong, Macao and Taiwan) in China during 2011—2021, we use the systematic GMM model, the mediation effect model and the dynamic threshold effect model to study the impact of the increase in the level of marketization on the high-quality development of agriculture. The study shows that: the increase of marketization level has a significant promotion effect on the high-quality development of agriculture, but excessive marketization will reduce this promotion effect; the impact of the increase of marketization level on the high-quality development of agriculture is heterogeneous in terms of the different dimensions of high-quality development of agriculture and the marketization level, as well as in terms of the analysis of different regional perspectives; the increase of the marketization level can have a significant impact on the high-quality development of agriculture through the two mediating paths of technological innovation and industrial structural adjustment. In the process of promoting high-quality agricultural development, government financial support for agriculture and marketization level enhancement have complementary roles. In this regard, China should improve the level of marketization and promote the high-quality development of agriculture from the following aspects: first, deepen the reform and give full play to the positive role of the market; second, implement policies according to the needs and improve the pertinence of marketization; third, stimulate innovation and smooth the path of marketization; fourth, complement each other’s strengths and promote the synergy between the market and the government.