The small modular liquid-metal fast reactor (SMFR) is an important component of advanced nuclear systems. SMFRs exhibit relatively low breeding capability and constraint space for control rod installation. Consequently, control rods are deeply inserted at beginning and are withdrawn gradually to compensate for large burnup reactivity loss in a long lifetime. This paper is committed to investigating the impact of control rod compensation operation on core neutronics characteristics. This paper presents a whole core fine depletion model of long lifetime SMFR using OpenMC and the influence of depletion chains is verified. Three control rod position schemes to simulate the compensation process are compared. The results show that the fine simulation of the control rod compensation process impacts significantly the fuel burnup distribution and absorber consumption. A control rod equivalent position scheme proposed in this work is an optimal option in the trade-off between computation time and accuracy. The control position is crucial for accurate power distribution and void feedback coefficients in SMFRs. The results in this paper also show that the pin level power distribution is important due to the heterogeneous distribution in SMFRs. The fuel burnup distribution at the end of core life impacts the worth of control rods.