Improving farmer cooperatives’ operating performance is essential for their economic sustainability and for promoting sustainable agricultural development. Despite the prominent role of benefit distribution and asset specificity in cooperation organizations, their impact on performance remains controversial, and the relationship between the three is unclear. This study focuses on cooperative benefit distribution in terms of their rebates (first and second rebates) and investigates the relationship between asset specificity, cooperative rebate and operating performance. The results show that both the first and second rebates have a positive impact on operating performance and play substitutive roles in increasing operating performance. Physical asset specificity (PAS) impacts first rebates positively, whereas human asset specificity (HAS) impacts first rebates negatively. PAS has a positive effect on operating performance whereas HAS has no significant influence on operating performance. Furthermore, the first rebate mediates the relationship between PAS and operating performance and suppresses the relationship between HAS and operating performance. These findings provide support for developing relevant policies to improve cooperative performance and sustainability.