To address the difficulty in predicting the Passive Intermodulation(PIM) of waveguide flange connections caused by micro-contact randomness, the fluctuations in both PIM and DC contact resistance at these joints are investigated. Experimental results demonstrate that, upon repeated connections, both PIM and DC contact resistance exhibit stochastic variations; moreover, the PIM level generally decreases as the DC contact resistance diminishes. To uncover the origins of these fluctuations, a Monte Carlo model for PIM at waveguide flanges is developed based on existing theories of PIM in electrical contacts. The numerical results agree well with experimental data, theoretically confirming that the random distribution of contact pressure during successive connections is a primary source of PIM variability in waveguide flange joints.