To reduce the congestion or wasted space caused by neglected space of buffer, the collaborative optimization of buffer allocation problem and facility layout problem was presented. Based on continuoustime Markov stochastic process theory, a queuing network node state model was established to solve utilization rate of facilities. A collaborative optimization model was built considering the utilization rate of facilities, material handling distance and floor area. The collaborative optimization model was calculated using improved NSGAⅡ. A case study of diesel engine cylinder block processing line was provided to prove the effectiveness of the proposed method.