At present, a cooperative process hypothesis is used to explain the supply of enzyme (class III peroxidases and/or laccases) and substrates during lignin polymerization. However, it remains elusive how xylem cells meet the needs of early lignin rapid polymerization during secondary cell wall formation. Here we provide evidence that a mitochondrial ascorbate peroxidase (PtomtAPX) is responsible for autonomous lignification during the earliest stage of secondary cell wall formation in Populus tomentosa. PtomtAPX was relocated to cell walls undergoing programmed cell death and catalysed lignin polymerization in vitro. Aberrant phenotypes were caused by altered PtomtAPX expression levels in P. tomentosa. These results reveal that PtomtAPX is crucial for catalysing lignin polymerization during the early stages of secondary cell wall formation and xylem development, and describe how xylem cells provide autonomous enzymes needed for lignin polymerization during rapid formation of the secondary cell wall by coupling with the programmed cell death process.