ABSTRACT Food processing operations play a significant role in the residual levels. Therefore, investigations into the fate of residues on food and their by-products are necessary to ensure food safety. We established an analytical method for the determination of kasugamycin residual levels on whole citrus and processed samples obtained from two sites using high-performance liquid chromatography coupled with tandem mass spectrometry. Furthermore, risk assessment also conducted to evaluate the chronic diet risk by TMDI-NEDI model. The results suggested that the half-life of kasugamycin in whole citrus and pulp was between 8.56–13.39 days, and 10.08–13.03 days in citrus. Additionally, the effects of commercial processing (washing, squeezing, refined filtration, high temperature instantaneous sterilisation, concentration, and centrifugation) on residual were also investigated, which indicated processing factors (PFs) values decreased in all processing samples, but increased in pomace. Additionally, the potential dietary risk in citrus was systematically evaluated by two risk assessment models, the entire NEDI is lower than the maximal ADI. These results demonstrated that the entire procedure can reduce residual kasugamycin in the concentrated juice. Regrading of risk assessment models indicated that the presence of residual kasugamycin in citrus and its processing products poses a minimal risk to human health.