The existing studies have primarily discussed the impact of land certification on farmers’ land transfer behaviors, neglecting its potential for centralized transfer under the orientation of optimizing land utilization and allocation efficiency. This study employed the Probit model, Propensity Score Matching method, and IV-Probit model to explore the effects and underlying mechanisms of land certification on centralized transfer based on the China Land Economic Survey data, especially emphasizing the roles of timing, inequality, and governance. Among transfer-out households, land certification increases the likelihood of farmers adopting centralized transfer rather than decentralized transfer. After considering the differential influence exerted by the timing of certification, the earlier the households obtain the land contract management certificates, the greater the positive impact. This phenomenon can be explained from the dual perspectives of economy and governance, including rural industrial development and rural governance performance. In the heterogeneity analysis, we focused on land inequality, farmers’ risk preference, and village governance teams’ capacity. Land certification mainly benefits farmers facing weak land inequality or low-risk preference, as well as those in villages with highly educated cadres. In the new round of land certification program, our findings provide new insights for continuously optimizing land utilization and allocation.