Based on the survey data of grain farmers in Shandong Province and Hubei Province, this paper analyzes the contractual governance logic and relational governance logic underlying farmland ecological protection by land transferees, and examines the relationship between the two behavioral logics. The empirical study focusing on fertilizer reduction demonstrates that transferees’ fertilizer application reduction follows both contractual and relational governance logics. Compared to informal contracts and weak-tie land transfers, formal contracts and strong-tie transfers can effectively reduce transferees’ fertilizer use. For transferees with low fertilizer application levels, contractual governance exhibits a more pronounced reduction effect, while relational governance leads to stronger reduction effects for those with medium-high fertilizer application levels. Further research reveals that different combinations of contractual and relational arrangements have different effects on fertilizer reduction outcomes among transferees, showing that the reduction effect of formal contracts and strong relationship transfers is not absolute. Specifically, in the strong relationship transfers, informal contracts can reduce fertilizer use more effectively than formal contracts; while for formal contract, the weak relationship transfers can be more effective in reducing the fertilizer application than the strong relationship transfers. Therefore, while promoting the contractual and standardized transfer of agricultural lands, it is also crucial to leverage the endorsement and coordination potential of the relational governance, and establish a synergistic relational-contractual governance mechanism to stimulate transferees’ participation in farmland ecological protection.