•The thermal stability and pyrolysis mechanism of cured BPR are investigated.•The high char yield of BPR results from the formed phenyl borates during curing.•Boron oxide is formed on the surface of carbonized product during pyrolysis.•The formed boron oxide revealed the cleavage of O–C bonds from phenyl borates.•The graphitization degree and graphite crystallites of PR are improved by introducing boron. Boron-containing phenolic resin (BPR) is a kind of the ablative resins with high-performance. Due to the lack of the exact knowledge concerning the pyrolysis mechanism of BPR, its development and application are greatly impeded. In the present paper, the chemical structure of the cured BPR and its structural evolution at high temperatures are investigated to clarify the reason for the high char yield of BPR. The results indicate that the high char yield of BPR is mainly attributed to the phenyl borates formed during curing, which can block parts of phenolic hydroxyl groups, and effectively inhibit their thermal decomposition reaction. Boron oxide is formed on the surface of carbonization products by the cleavage of O–C bonds from phenyl borates via pyrolysis, which avoids the release of volatile carbon dioxide and reduces the development of micro-structural defects of carbonization products. Introducing boron into PR improves the graphitization degree and graphite crystallites of carbonization products, which promotes the formation of a more ordered glassy carbon during pyrolysis. This study provides a new vision for the understanding of the high char yield of BPR, which makes it possible to develop a new ablative resin through molecular design.