This paper theoretically analyzes the mechanism and service boundaries of the De Soto effect of the land registration, and discusses the paradox of China’s farmland mortgage in practice, so as to comprehensively evaluate whether China’s farmland financial reform can effectively alleviate the financing constraints of the rural credit market after the land registration, and thus the discussion is extended to innovating rural financing models to meet the financing needs of farmers. The analysis shows that the De Soto effect of the land registration cannot be fully exerted in the rural credit market, and its role in alleviating financing constraints is “effective” on the credit demand side, but “limited” on the credit supply side, and farmers’ financing demand cannot be effectively translated into actual supply. The analysis of the legal predicament and principal-agent problems of China’s farmland mortgage at the present stage demonstrates that there are paradoxes in the practice of China’s farmland mortgage reform, which has limited the De Soto effect of the land registration on the credit supply side: First, the external environment has not yet established supporting systems and measures to serve the mortgage of farmland, resulting in the fact that farmland management rights cannot become qualified collateral recognized by financial institutions; second, the inconsistent dual objectives of rural commercial banks and the information asymmetry between them and farmers leads to the “failure” of agricultural land mortgage loans. Finally, it is recommended to strengthen the top-level design of farmland financial reform, and deepen the effective integration between farmland financial reform and alleviation of financing constraints. In addition, innovative models can be explored to alleviate the dilemma of rural financing constraints from the perspective of mortgage substitution mechanism.