Heterosis is extensively utilized in the two-line hybrid breeding system. Photo-/thermo-sensitive genic male sterile (P/TGMS) lines are key components of two-line hybrid rice. TGMS lines containing tms5 have significantly advanced two-line hybrid rice breeding. We cloned the TMS5 gene and found that TMS5 is a tRNA cyclic phosphatase that can remove 2′,3′-cyclic phosphate (cP) from cP-ΔCCA-tRNAs for efficient repair to ensure maintenance of mature tRNA levels. tms5 mutation causes increased cP-ΔCCA-tRNAs and reduced mature tRNAs, leading to male sterility at the restrictive temperatures. However, the regulatory network of tms5-mediated TGMS remains to be elucidated. Here, we identified that an E3 ligase OsHel2 cooperates with TMS5 to regulate TGMS at the restrictive temperatures. Consistently, both the accumulation of 2′,3′-cP-ΔCCA-tRNAs and insufficiency of mature tRNAs in tms5 mutant were largely recovered in the tms5 oshel2-1 mutant. A lesion in OsHel2 results in partial readthrough of the stalled sequences, thereby evading ribosome-associated protein quality control (RQC) surveillance. Our findings reveal a mechanism by which the OsHel2 impede readthrough of stalled mRNA sequences to regulate male fertility in TGMS rice, thus providing a paradigm for investigating how disorders in the components of the RQC pathway impair cellular functions and lead to diseases or defects in other organisms.