The pultrusion process exhibits higher production efficiency compared to other manufacturing processes for FRP composites. Pultruded FRP composite profiles are utilized widely in civil engineering due to their excellent performance. However, there are some non-uniformities, such as mat wrinkles, in the cross-section of pultruded FRP profiles because of the pultrusion process itself. Some previous studies have explored the impact of non-uniformity on mechanical performance, but it is not clear how non-uniformity influences diffusion behavior. To that end, a distilled water immersion experiment of pultruded plates under room temperature was conducted. All samples were weighed periodically to obtain weight gain curves. CT scanning, image segmentation, and finite element simulations were performed on the pultruded plate. Simulation results were in good agreement with experimental results, verifying the simulation approach. A case study was then carried out to analyze the effect of the internal CSM layer on moisture diffusion. The simulation results showed that for pultruded plates with the internal CSM layer, the non-uniformity can accelerate moisture diffusion process in the \(z\) direction. However, the diffusion behavior in the \(y\) direction is not influenced obviously. The result is useful for the design and optimization of cross-sections considering the durability of pultruded FRP composites in humid environments.