Ecological compensation for cultivated land protection plays an important role in ensuring the continuous supply of ecological functions of cultivated land and internalizing the externalities of cultivated land protection. Based on the logic of "trinity" protection of cultivated land, this study introduces the landscape pattern index, takes into account the differences in spatial configuration of cultivated land, establishes a multi-scale accounting system for the ecological service value of cultivated land in watersheds, and formulates the ecological compensation amount for differential protection of cultivated land in watersheds by combining the ecological carrying capacity of cultivated land, and proposes a financial transfer path. The research results show that: 1) From 2000 to 2020, the ecological value of cultivated land in the Liaohe River basin of Jilin Province was gradually revealed, and the spatial heterogeneity was significant, with the overall northern region higher than the southern region, and the middle and lower reaches of the region being the main contributing region to the ecological value of cultivated land. 2) As of 2020, the cultivated land in the basin as a whole is in ecological surplus, with a surplus of 484.5 thousand hectares, and the supply and demand of cultivated land in various districts and counties are characterized by “surplus in counties (cities) and deficit in districts”. 3) There are significant spatial differences and scale-dependent effects in the amount and mode of ecological compensation for cultivated land protection in the watershed. The total amount of compensation for cultivated land protection in the watershed is 1.350 billion yuan, and the amount of compensation for cultivated land protection in each district and county is -0.003 billion ~0.657 billion yuan. Therefore, the establishment of the ecological compensation mechanism for cultivated land protection should take into full consideration the ecological service value of cultivated land, carrying capacity, regional differences, scale-dependent characteristics, and other relevant factors, so as to improve the precision and effectiveness of compensation. At the same time, horizontal and vertical financial transfers of cultivated land for ecological compensation can be realized through the establishment of intermediary platforms and other means.