The heat resistance of existing phenolic resins cannot meet the requirements of the increasingly harsh spaceflight environment. Boron and silicon have been added to phenolic resins to improve the char yields. However, achieving both a high initial decomposition temperature and an outstanding char yield remains challenging. This study presented a strategy to regulate the methylene types of boron-containing phenolic resin (TBPR) by trisilanolphenyl polyhedral oligomeric silsesquioxane (TPOSS) and NaOH. Thermogravimetric analysis (TGA) in nitrogen of cured TBPR displayed remarkable thermal stability with an initial decomposition temperature of 450.0 °C and a char yield of 75.8 %. The effect of TPOSS and NaOH on the TBPR structure were further investigated using nuclearmagneticresonance (NMR) analysis and densityfunctionaltheory(DFT) calculation. The results indicated that TPOSS could attract sodium phenate and formaldehyde through hydrogen bonds, and greatly reduced the energy barrier of the phenol–formaldehyde resin para-addition. The formation of more p-p’ type methylene structures of phenolic resin profoundly contributed to the outstanding initial decomposition temperatures and char yield. TBPR matrix transformed into a stronger protective char layer, forming an effective thermal protection barrier. As a result, the mechanical strength and ablative resistance of the fiber-reinforced CF/TBPR composites were enhanced by the excellent thermal stability of TBPR matrix.