Photovoltaic thermal (PVT) collector-based active cooling technology makes it possible to increase the efficiency of PV solar cells and meanwhile generate heat through the direct conversion of solar irradiation into electricity. Hence, this study presents a detailed numerical analysis of the thermal performance of PVT solar collectors integrated with flax fibers as natural porous materials. To achieve this goal, a cooling channel is proposed, which contains porous flax fiber materials doping in pure water as a cooling fluid for the photovoltaic panels. A particular focus of this research is emphasized on the effects of the thickness of the porous material layer (5−50 mm), the solar flux (50−1000 W/m2), and the flow rate of coolant (0.40−1.0 m/s), to determine the best thickness of the porous material and the cooling fluid flowrate that achieves the highest performance of photovoltaic panels. The simulations are performed using ANSYS software, Navier Stokes equations, and Darcy-Brinkman-Forchheimer porous model. Moreover, the thermal performance of the proposed PVT system cooled with water/porous flax fibers mixture is analyzed and compared with the PVT collector using pure water and air as a coolant. The results presented that the optimal design for maximization of the cooling of photovoltaic panels is attained by incorporating porous flax fibers materials with a thickness of 50 mm and 0.907 m/s cooling water flowrate. It is indicated that the Nusselt number is increased from 18.65 to 51.0, with an improvement of 173.46% as compared to the use of only pure water at the optimal conditions. Moreover, the thermal efficiencies of the PVT system are obtained as 69.58%, 50.02%, and 34.60% using water with a flax fibers layer, pure water, and air, respectively.