Thermally stable high-performance phenolic resin aerogels (PRAs) are of great interest for thermal insulation because of their light weight, fire retardancy and low thermal conductivity. However, the drawbacks of PRA synthesis, such as long processing time, inherent brittleness and significant shrinkage during drying, greatly restrict their wide applications. In this work, PRAs were synthesized at ambient pressure through a near-net shape manufacturing technique, where boron-containing thermosetting phenolic resin (BPR) was introduced into the conventional linear phenolic resin (LPR) to improve the pore characteristics, mechanical properties and thermal performances. Compared with the traditional LPR-synthesized aerogel, the processing time and the linear shrinkage rate during the drying of the PRAs could be significantly reduced, which was attributed to the enhanced rigidity and the unique bimodal pore size distribution. Furthermore, no catastrophic failure and almost no mechanical degradation were observed on the PRAs, even with a compressive strain of up to 60% at temperatures ranging from 25 to 200 °C, indicating low brittleness and excellent thermo-mechanical stability. The PRAs also showed outstanding fire retardancy. On the other hand, the PRAs with a density of 0.194 g/cm3 possessed a high Young's modulus of 12.85 MPa and a low thermal conductivity of 0.038 W/(m·K).