In recent decades, the development of dialysis techniques has greatly improved the survival rate of renal failure patients, and peritoneal dialysis is gradually showing dominance over hemodialysis. This method relies on the abundant membrane proteins in the peritoneum, avoiding the use of artificial semipermeable membranes, and the ion fluid transport is partly controlled by the protein nanochannels. Hence, this study investigated ion transport in these nanochannels by using molecular dynamics (MD) simulations and an MD Monte Carlo (MDMC) algorithm for a generalized protein nanochannel model and a saline fluid environment. The spatial distribution of ions was determined via MD simulations, and it agreed with that modeled via the MDMC method; the effects of simulation duration and external electronic fields were also explored to validate the MDMC algorithm. The specific atomic sequence within a nanochannel was visualized, which was the rare transport state during the ion transport process. The residence time was assessed through both methods to represent the involved dynamic process, and its values showed the temporal sequential order of different components in the nanochannel as follows: H2O > Na+> Cl−. The accurate prediction using the MDMC method of the spatial and temporal properties proves its suitability to handle ion transport problems in protein nanochannels.