Most allocation model of control rights in the existing public-private partnership(PPP) projects assumes that private sector is self-serving economic man, ignoring its reciprocal preference. Therefore, through inplanting reciprocal preference into cooperation output effect of private sector, this paper studies and builds the allocation model of control rights of private sector in PPP projects. The results show that the optimal allocation range of control rights of private sector has a positive correlation with reciprocal preference input cost while a negative correlation with cooperation degree. When taking reciprocal preference into consideration, the share of control rights has a prominent role in promoting the input level of private sector and the output level of cooperation. At the sametime, only being limited in a certain range can the control rights have such effect. Exclusive or excessive control rights will lead to inefficiency of input.