The frequent terrorist attacks in subways has dramatically increased the necessity and importance of security check systems (SCSs). The implementation of a SCS in China has successfully eliminated lots of potential safety hazards. However, the excessive waiting time due to the SCS is also an issue. SCS efficiency is greatly affected by the length of the conveyer belt of the X-ray machine (CBXM). A scheme for optimizing the CBXM length to accommodate different passenger flows is proposed in this paper. A modeling framework is developed for associating the CBXM length with the queuing waiting time based on a M/M/1/N queuing model. The optimal scheme of CBXM length calculated from the model demonstrates that the passenger queuing time is saved by 15.7%, 16.0%, and 23.3% with the passenger arrival rate of 4000, 5000, and 6000, respectively, greatly reducing queuing crowdedness. The scheme can be used to select X-ray machines for subway stations by their passenger arrival rates. In addition, the findings of this paper could be a crucial supplement and perfect the design code of subway SCSs.