Decay calculations play an important role in reactor physics simulations. In particular, the isotopic decay of the burned fuel during refueling is important for predicting the startup reactivity of the following burn-up cycle. In addition, there is a growing interest in high-fidelity simulations where the mesh in the burn-up region can involve millions of regions. However, existing models repeatedly solve the same Bateman equations for each region, which is a waste of calculational resources. RMC is a Monte Carlo neutron transport code developed for advanced reactor physics analysis including criticality calculations and burn-up calculations. This paper presents a decay calculation method named the Decay Chain Method (DCM) to optimize the RMC code for large-scale decay calculations. Unlike traditional methods, the Decay Chain Method solves the Bateman equations one decay chain at a time rather than one region at a time. The decay calculation in the burn-up mode then treats the decay steps as zero power burn-up steps with some optimized calculational methods to further reduce the calculational time. These methods were evaluated for a single pin example and for a Virtual Environment for Reactor Applications (VERA) full-core example. The calculations for the single pin example verify the accuracy of the decay step treatment in the burn-up mode and show the improved efficiency. The single pin is divided into 1–1,000,000 decay regions to study the efficiency differences between the Transmutation Trajectory Analysis (TTA) and DCM methods. Both methods have a linear complexity with respect to the number of regions but DCM costs just one-sixtieth of the TTA time. In the simplified VERA full core example, the DCM method reduces the decay calculation time to 0.32 min from 75.26 min while the accuracy remains unchanged.