The imbalance of rural human–land relationships has become a notable problem in China’s urbanization process. The dual urban–rural system is widely regarded as the crucial factor contributing to this problem in China. Although the significance of institutional forces has been substantially recognized, the rural homestead system seems to be generally under-evaluated in this issue. Most of the previous literature focuses on the dual household registration system, while the effects and the detailed mechanisms of the rural homestead system on human–land relationships lack depth in research. The objective of this research is to help fill this gap in the literature on the complex effects and the detailed mechanisms of the rural homestead system on rural human–land relationships. In view of this, this paper establishes a conceptual framework on the basis of land function theory and public domain of property rights theory and proposes two mechanism hypotheses: one is the land attachment mechanism of farmers’ rights and interests (LAM), the other is the land finance preference mechanism of local governments (LFPM). Then, this article examines them empirically using the panel model with the data of 41 cities from 2010 to 2021 in the Yangtze River Delta of China. The main conclusions are as follows: (1) LAM promotes the imbalance of rural human–land relationships due to the attachment of farmer’s social security rights and property expectant interests to the rural homesteads; (2) LFPM drives the imbalance of rural human–land relationships, owing to both the preference of land transfer revenue and the exclusion of rural migrants’ citizenship financial cost on local governments; (3) the moderating effects suggest that LFPM can strengthen the effect of LAM, and the spatial Durbin model results show that both LAM and LFPM have spatial spillover effects. It is hoped that the findings will provide a reference for deepening the rural homestead system reform.