Agriculture sustainability assessment is conducive to promoting sustainable agriculture construction and sustainable development. Modern agriculture and modern small-peasant production have different requirements for agriculture sustainability. Related studies provided assessment frameworks for many parts of the world. However, existing frameworks have distinct limitations and are not applicable to modern small-peasant economy (MSE) areas, such as China. The purpose of this study is regarding China as an example to construct a healthy farmland system assessment framework (HFSAF), to assess smallholder farmland systems’ sustainability. HFSAF’s theoretical basis, indicator system, data preparation methods, multi-level aggregation rule and results description method are presented in this paper. HFSAF is a multi-level indicator system with adjustable parameters, covering environment, economy and society aspects, including three dimensions, nine visions, 15 themes and 40 basic indicators. Taking Da’an City, Jilin Province, China as the study area to implement HFSAF. The assessment results prove HFSAF can be used to assess agricultural sustainability in MSE areas with limited agro-resource supplies, to assist the sustainable decision-making and regional agriculture remold.