The atomic structure, glass formation process and diffusion mechanism of Pd100-xSix (x = 10, 20, 30, 40 and 50) alloys during rapid solidification have been investigated by molecular dynamics simulations using embedded atom method potentials. The structure factors, total (or Pd90Si10) and partial pair distribution functions calculated for Pd80Si20 bulk metallic glass are in good agreement with the experimental/other data. Bond angle distribution function, Honeycutt-Andersen index and Voronoi tessellation analysis have revealed that the increasing Si amount caused a decrease in the number of icosahedral-like clusters and an increase in the number of crystal-like clusters. The majority of icosahedral-like clusters in the systems are mostly composed of Pd-centered clusters, suggesting that Pd has an effective role in the glass formation process in Pd-Si systems. It has been observed that the mobility of Si atoms decreases in environments with more Pd atoms. The critical temperature and T0 temperature for Pd-Si liquids have been determined from the self-diffusion coefficients using the mode-coupling theory and the Vogel-Fulcher-Tammann law, respectively. The present findings show us that the Pd70Si30 compound has a critical importance in terms of the glass formation process, which is consistent with experimental observations. We hope that the results will contribute to understanding the Si effect on the atomic local structure of Pd-Si systems and will encourage research on many properties of these systems, such as their mechanical properties.