Fully utilizing farmers’ human capital investment to enhance their income growth holds significant practical implications for improving the quality of farmers’ income, strengthening their capacity for sustainable income increase, and achieving common prosperity. Based on a data from 110 prefecture-level cities in the Yangtze River Economic Belt from 2010 to 2021, this paper adopts a two-way fixed-effect model to analyze the impacts of farmers’ human capital investment on their incomes, to explore its group heterogeneity and regional heterogeneity in depth, and to examine the moderating effect and the mechanism of urbanization. In addition, this paper also uses the threshold effect model to analyze the nonlinear impacts of farmers’ human capital investment on their incomes. Results show that farmers’ human capital investment has a significant positive impact on their income, but its impact effect is characterized by a typical double thresholds. Heterogeneity analysis suggests that the income-enhancing effect of farmers’ human capital investment is more obvious for middle- and high-income farmer groups and has the most significant boost for farmers in the lower reaches of the Yangtze River. Farmers’ health investment can lead to increased incomes for various groups of farmers. Urbanization plays a positive moderating role in the impacts of farmers’ human capital investment on their income. Therefore, this paper provides the following suggestions: shifting more efforts to increase investment in rural public education, improving the health literacy of the entire population and the health level of the population, supporting the construction of rural transportation networks, promoting the integrated development of urban and rural areas, advancing the urbanization process of counties in a categorized and orderly manner, with a focus on upgrading the ability to invest in the human capital of underdeveloped regions and low-income farmer groups, and building a mechanism for stable and sustainable income growth for farmers.