Thermosensitive genic male-sterile (TGMS) lines, which are male-sterile at restrictive (high) temperatures but male-fertile at permissive (low) temperatures, have been widely used in breeding two-line hybrid rice (Oryza sativa L.). Here we find that mutation of ？thermosensitive genic male sterile 5 (？tms5) in rice causes the TGMS trait through a loss of ？RNase Z^S1 function. We show that ？RNase Z^S1 processes the mRNAs of three ubiquitin fusion ribosomal protein L40 (Ub_L40) genes into multiple fragments in vitro and in vivo. In ？tms5 mutants, high temperature results in increased levels of Ub_L40 mRNAs. Overaccumulation of Ub_L40 mRNAs causes defective pollen production and male sterility. Our results uncover a novel mechanism of ？RNase Z^S1-mediated Ub_L40 mRNA regulation and shows that loss of this regulation produces TGMS in rice, a finding with potential applications in hybrid crop breeding.