This study explores the major reasons for Chinese small dairy farms to accept the new organization structure, dairy complex (DC), and the discrepancies between the actual effect and farmers’ perceptions. Our results show that the frequency of milk refusal, herd scale and farmers’ age contribute to farmers’ decision in accepting DCs, while sale price and disease prevention do not have significant influence. Independent farmers’ perceived effects and the actual effects of DCs in improving raw milk safety and price are consistent, but there exists misperception of DCs’ effect in disease prevention.