Thermo-sensitive genic male-sterile (TGMS) lines are fertile at lower temperatures but male sterile above a critical sterility-inducing temperature (CSIT), which varies substantially across TGMS lines. Such lines are valuable resources for breeding two-line hybrid rice (Oryza sativa). However, as their utility is restricted by the CSIT, understanding its regulatory mechanisms has crucial breeding-associated implications. The thermo-sensitive genic male sterility 5 (tms5) mutation is common to most TGMS lines. We previously revealed that tms5 mutants failed to recycle cyclic phosphate (cP)-containing ΔCCA-tRNAs, particularly in pollen mother cells, resulting in fewer mature tRNAs, thereby causing TGMS. However, the CSIT-regulatory network in the tms5 lines remains unelucidated. Here, we characterized the CSIT-related ribosome-associated quality control 1 (OsRqc1) gene. OsRqc1 binds to the 60S ribosomal subunits and functions in ribosome-associated quality control. It also regulates the CSIT in tms5 lines by assisting OsVms1 in recruiting these subunits to generate cP-ΔCCA-tRNAs. Variations in a 6-bp repeat in the 5′ untranslated region of OsRqc1 in rice subspecies affect its transcription, thereby altering the CSIT in tms5 lines. These findings reveal the role of an OsRqc1-OsVms1 module in regulating CSIT, providing valuable insights into genetic variations in OsRqc1. Such results may facilitate the molecular breeding of rice two-line hybrid tms5 lines with specific CSITs, which can adapt to regions with different environments.