The development of high toughness as well as flame‐retardant polylactic acid (PLA) materials is important for expanding the practical applications. Herein, a type of high toughness PLA composites with improved flame retardancy was developed through combining modified carbon nanotubes (CNT) and polysiliconoxaborane (PBSi) with PLA matrix. The optimal PLA composite (PLA/PBSi/CNT‐3.0) exhibited excellent crystallization degree (18.7%), thermal stability (the Ea significantly increased), flame retardancy (the values of peak heat release rate (PHRR) polarized optical microscopy and total heat release (THR) decreased to 287.1 W/g and 15.5 kJ/m2, respectively), and mechanical properties (the elongation at break increased to 149.5%, with an increasement of 1745.7%) due to the combined action of flexible chain segments and hydrogen bonding interactions. Furthermore, the toughening mechanism of the PLA/PBSi/CNT composites was illustrated and attributed to the combination of flexible SiOBO segments and two dominant energy dissipation processes (the breakage of hydrogen bond and the destruction of microcrystals). Overall, this work provided a facile approach for improving the toughness and flame retardancy of PLA, which was conducive to expanding the application range of PLA.