Fiber-reinforced aerogel composites are widely used for thermal protection. The properties of the fibers play a critical role in determining the structure and properties of the final aerogel composite. However, the effects of the fiber's characteristics on the structure and properties of the aerogel composite have rarely been studied. Herein, we prepared quartz fiber felt-reinforced silica-polybenzoxazine aerogel composite (QF/PBSAs) with different fiber diameters using a simple copolymerization process with the ambient pressure drying method. The reasons for the effects of fiber diameter on the structure and properties of the aerogel composites were investigated. The results showed that the pore structure of the aerogel composites was affected by the fiber diameter, which led to significant changes in the mechanical behavior and thermal insulation performance. At room temperature, pore structure and density were found to be the main factors influencing the thermal conductivity of the composites. At elevated temperatures, the radiative thermal conductivity (λr) plays a dominant role, and reducing the fiber diameter suppressed λr, thus decreasing the thermal conductivity. When the QF/PBSAs were exposed to a 1200 °C butane flame, the PBS aerogel was pyrolyzed, and the pyrolysis gas carried away a large amount of heat and formed a thermal barrier in the interfacial layer, at which time λr and the pyrolysis of the PBS aerogel jointly determined the backside temperature of the composites. The results of this study can provide valuable guidance for the application of polybenzoxazine aerogel composites in the field of thermal protection.