Regional collaboration plays a critical role in ecosystem service conservation and human wellbeing. However, its impacts on local ecosystem services and household livelihood have not yet been investigated. We select two regional collaboration projects (“Afforestation” and “Return Paddy to Dry Land”) in the upper watershed of Miyun reservoir in Beijing, where water resource conservation and regional economic development are two great challenges, to assess their effects on ecosystem services and household livelihood. To accomplish these, we (1) utilize the InVEST model to map the ecosystem services changes (water yield, erosion control, water purification) of regional collaborations; (2) and assess the changes of financial, material, human and social capitals in RPDL project area. Our results showed that “Afforestation” decreased water yield by 14%, while increasing erosion control and water purification services by 33% and 63%, respectively. “RPDL” can only change these services slightly. However, It can significantly change household livelihood. Participants own more assets and educational expense, decrease more firewood expense, pesticide and fertilizer utilization, and increase more income proportion of migrating work in comparison with non-participants. Our research provides a feasible method for comprehensive assessment of regional collaboration effects on ecosystem services and household livelihood.