This study presents a comparative analysis of the quasi-transient neutronic behavior during the fuel draining process of two Molten Salt Reactors (MSRs): the Molten Salt Fast Reactor (MSFR) and the Dual Fluid Reactor (DFR). The MSFR, as a pool-type MSR, and the DFR, as a tube-type MSR, exhibit unique advantages in passive safety, inherent stability, and fuel breeding. The fuel draining process is crucial for ensuring the safe shutdown of the reactor in case of emergencies. The neutronic calculations were performed using the Monte Carlo code Serpent, simulating the fuel reduction process and analyzing the core effective multiplication factor, neutron flux distribution, neutron energy spectrum structure, and group constants. The results indicate that the neutron spectrum structure of the MSFR remains relatively stable with fuel reduction, whereas the DFR shows a trend towards lower energy spectra and the emergence of a new spectral peak in the 0.1 eV–1 eV range. The effective multiplication factor (keff) for both reactors decreases as fuel is drained, with the MSFR showing a less pronounced decrease due to its larger void space compared to the DFR, which has a complex internal structure. The study provides insights into the neutronic behavior of MSRs during the draining process, which is essential for the design and safety assessment of MSRs. The findings suggest that the MSFR’s single-group diffusion model is feasible for neutronic analysis, while the DFR requires a more detailed model to account for its complex geometry and neutron moderation effects. This comparative study contributes to the understanding of the physical processes involved in MSR fuel draining and aids in the optimization of the draining system design.