Abstract The synthesis of silicon quantum dots (SiQDs) via thermal pyrolysis is considered promising due to its cost-effectiveness. The etching process in this method has the potential to control the size of SiQDs precisely and has thus garnered attention. However, there are varying observations regarding the effect of etching duration on SiQD size. Additionally, the impact of dioxonium hexafluorosilicate (DH), a byproduct of the etching process, on the photoluminescence (PL) quantum yield (QY) of SiQDs remains unclear. This study investigates the effect of etching duration on the physical and optical sizes as well as the PLQY of SiQDs. The results indicate that extending the etching duration decreases the physical size of SiQDs, while the optical size initially increases slightly before decreasing. The SiQDs transition through three phases with increasing etching duration: oxidation removal, shallow over-etching, and deep over-etching. Both amorphous silicon (a-Si) in the oxidation removal phase and DH in the deep over-etching phase act as non-radiative recombination centers, thereby reducing the PLQY of SiQDs. Therefore, optimizing the etching duration to achieve the shallow over-etching phase is essential. This study provides new insights into the effects of etching duration on SiQD size and PLQY, aiding in the preparation of higher-quality SiQDs.