In this study, molecular dynamics simulations were employed to study the mechanism of the transport of hydronium ions in a Nafion membrane incorporated with SiO2 nanoparticles at 300 K. The SiO2 contents were 1.55 wt%, 4.51 wt% and 7.3 wt%, respectively. The Nafion membrane was highly hydrated, with a water content lambda = 28. The conductivity of proton in this highly hydrated Nafion/SiO2 membrane was simulated. Through the analysis, we estimated that the conductivity ranged from 0.023 to 0.075 S cm(-1), which was close to the experimental measured values. The conductivity was decreased with increasing SiO2 content, a trend that agreed well with the experimental measurements, and the origin of the increase in the diffusion constant of water with the increase in SiO2 content was discussed. Our analysis showed that the Grotthuss mechanism is the most probable mechanism for the proton transport in these highly hydrated Nafion/SiO2 membranes.