Small pressurized water reactors usually adopt the soluble-boron-free core design, relying on burnable poisons and control rods to regulate the excess reactivity. The spatio-temporal non-uniformity introduced by the long-term insertion of control rods into the core and their movement during the reactor’s lifetime has a significant impact on the reactor’s characteristic parameters. This paper focuses on the small pressurized water reactor core with helical-cruciform metallic fuel, considering the control rod compensation movement, and optimizes the power distribution during the reactor’s lifetime. A burnup depth zoning method for optimizing the arrangement of burnable poisons in 2D/3D cores has been developed and validated. This method combines genetic algorithms with the 2D Method of Characteristic (MOC) assembly calculations to establish an assembly library of optimal burnable poison concentration distributions at corresponding burnup depths, ensuring minimum residual penalty and initial keff. Through iterative calculations of core burnup and the zoning arrangement of burnable poisons based on burnup depth, the optimal result for the 3D core burnable poison arrangement considering control rod movement is obtained. The results indicate that, after the core depletion calculation iterations without control rod insertion, the radial power peak factor of the optimal case is reduced by 14%, and the maximum average burnup depth of the fuel assemblies is reduced from 119.0 GWd/tU to 96.1 GWd/tU. After the core burnup iterations considering control rod movement, the maximum power peak factor during the optimal iteration step is reduced by 21.2%, and the maximum burnup depth is reduced from 149 GWd/tU to 119.4 GWd/tU.