In semiconductor manufacturing, a cluster tool consists of loadlocks, several processing chambers and a robot for transporting wafers. During wafer fabrication, a chamber needs cleaning for removing residual gases and solid particles to reduce risk of contamination wafer surface. Chamber cleaning makes the scheduling problem of cluster tools more complicated, which leads to deadlock. The method based on virtual wafer can avoid such problem, but this method also reduces chamber utilization. Aiming to improve the throughput of cluster tools with chamber cleaning, this paper modifies robot sequences and adjust the processing time of virtual wafer. Then, based on the time characteristics of the system, a linear programming model is established to achieve the optimal solution of scheduling. Finally, illustrative examples are given to verify the feasibility and effectiveness of the proposed method. Compared with the existing virtual wafer method, this method can effectively reduce the system cycle time and improve the production efficiency of dual-arm cluster tools with chamber cleaning.