This study investigated the effects of partially replacing expensive Mo with cheaper Nb on the microstructure and properties of high-strength low-alloy (HSLA) steel during reverse austenisation. The mechanical properties of the steel in the hot-rolled state were lower with a partial replacement of Mo by Nb. However, after pre-tempering and reheating and quenching, the strength increased greatly while the ductility and toughness did not decrease much. Thus, the negative effects of replacing Mo with Nb were mostly alleviated, and a good balance between strength, ductility and toughness was achieved. After heat treatment, the mass percentage of precipitates increased substantially, which helped to pin grain boundaries during austenisation. The percent of high-angle grain boundaries greatly increased while the average effective grain size decreased, which improved grain refinement. The results showed that combining a partial replacement of Mo by Nb with heat treatment allows the microstructure and mechanical properties of HSLA steel to be effectively controlled while improving the balance between cost and performance. These findings provide valuable insights into the preparation and design of steels with similar microstructures.