In most organisms, various physiological and behavioral functions are expressed rhythmically. Previous studies have shown that thermoperiod is an important factor affecting circadian clock-related genes that regulate insect locomotor activity. Bradysia odoriphaga Yang et Zhang (Diptera: Sciaridae) is an underground pest that attacks more than 30 crops but is especially damaging to Chinese chive. In this study, we analyzed adult eclosion time and Boper gene expression in B. odoriphaga as affected by temperature (cycling vs. constant temperature), insect stage, and adult body part. We found that the eclosion time and expression of the Boper gene changed during the temperature cycle but not under a constant temperature. Silencing of Boper expression significantly decreased the adult eclosion rate and significantly increased adult mortality and malformation. The findings indicate that thermoperiod alters Boper expression and regulates the eclosion rhythm.