As the largest emerging economy globally, China is facing crop-livestock disconnection, which causes unnecessary synthetic fertiliser use, local food and feed unsatisfied demand, and manure nitrogen (N) surplus. OBJECTIVE: We investigated how crop-livestock regional integration combined with inter-regional transportation of food, feed, and manure, can contribute to food self-sufficiency of easter China (whole and regional level) while avoiding manure N excess. We also investigated how this could increase the local soybean production without harming the self-sufficiency of other food commodities. METHODS: We proposed an optimisation model of integrated crop-livestock production in eastern China, including the production of food, feed, and livestock manure N in each region and the demand for food (according to healthy diet recommendations), feed and manure N. We optimised the supplier cost-benefit balance considering food and feed production, domestic transportation, and foreign trade, taking food and feed demand satisfaction and manure N surplus avoidance as constraints. This optimisation exercise was performed under different scenarios: optimisation without soybean subsidies (scenario O), optimisation with increasing soybean subsidies (scenario OS+). The two scenarios were compared with the baseline scenario B (non-optimised without soybean subsidies) using balance indices (BI, the gap between production and demand divided by demand) of food, feed, and manure N and transportation indices. RESULTS AND CONCLUSIONS: Results showed that, for the whole of eastern China, BI were positive for cereals (1.523), vegetables (2.789), meat (0.002), eggs (0.002), milk (0.102), and maize (0.244), and negative for manure N (−0.016) in scenario O. This indicated that most of the food and feed items except soybean were self-sufficient and manure N surplus was avoided after optimisation. Some regions lowered their self-sufficiency for some commodities. As soybean subsidies increased from 0 Yuan ‧ ton-‍1 to 6000 Yuan ‧ ton−1, the BI of soybeans increased by 66.37%. SIGNIFICANCE: Our results suggested that crop and livestock can be integrated in China for an improved level of food self-sufficiency and manure N surplus avoidance. However, regional self-sufficiency could not be achieved in all regions for all items, and transportation is necessary. In particular, three strategies seem relevant for policy-making: (i) decreasing livestock quantity, for strengthening feed self-sufficiency and avoiding manure N surplus; (ii) increasing soybean production through subsidies; (iii) reducing regional-level self-sufficiency and increasing the transportation for meat and eggs, which would avoid manure N surplus in densely populated regions, while decreasing the maize transportation. © 2024 Elsevier Ltd