The moisture diffusion behaviors of 3D woven composites exhibit non-Fickian properties when they are exposed to a hydrothermal environment. Although some experimental works have been undertaken to investigate this phenomenon, very few mathematical works on non-Fickian moisture diffusion predictions of 3D woven composites are available in the literature. To capture the non-Fickian behavior of moisture diffusion in 3D woven composites, this study first utilized a time fractional diffusion equation to derive the percentage of moisture content of a homogeneous material under hydrothermal conditions. A two-stage moisture diffusion model was subsequently developed based on the moisture diffusion mechanics of both neat resin and 3D woven composites, which describes the initial fast diffusion and the long-term slow diffusion stages. Notably, the model incorporated fractional order parameters to account for the nonlinear property of moisture diffusion in composites. Finally, the weight gain curves of neat resin and the 3D woven composite were calculated to verify the fractional diffusion model, and the predicted moisture uptake curves were all in good agreement with the experimental results. It is important to note that when the fractional order parameter α < 1, the initial moisture uptake will become larger with a later slow down process. This phenomenon can better describe non-Fickian behavior caused by initial voids or complicated structures.