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Due to the inherent safety and high mass/heat transfer efficiency of microreactor, the continuous micro-reaction technology has been widely applied in hazardous chemistry recently. In this work, a continuous ozonolysis system based on micro-packed bed reactors (µPBRs) was developed with the synthesis of benzaldehyde as a model reaction. The effects of operating variables (e.g., stirring time, molar ozone/olefin ratio, reaction pressure, reaction temperature and liquid residence time) on the olefins conversion and product distribution were investigated. Based on the experimental results, the optimum reaction conditions are as follows: stirring time 1 h, molar ratio of ozone to olefin 1.2, reaction pressure 0.1 MPa, and the reaction temperature ranging from − 15 to 10℃, as opposed to the low temperature (<-50℃) routinely employed for batch operation. In addition, the full conversion of styrene and a benzaldehyde yield of ~ 93% was observed with the liquid residence time of 3.8–30.8 s. Consequently, the flow ozonolysis technique upon µPBRs allows for a sustainable, safe and efficient approach to oxidize olefins to aldehydes/ketones compared to traditional methods.