Based on Nuctech radiography Monte Carlo simulation software NucRPD, three methods are developed to analyze the effect of the two-dimensional anti-scatter grid in the container CT inspection system with a 9MeV accelerator: target crystal pen tag method, scattered component tag method, and tomography image reconstruction method. Calculation results of the three methods all show that the profit of the two-dimensional anti-scatter grid in reducing scattered X-rays in this container CT inspection system is limited. It is suggested that the two-dimensional anti-scatter grid not to be used in the subsequent engineering implementation, which will greatly reduce not only the mechanical design difficulty of the detector and rotating gantry, but also the engineering cost.