The reaction of isoprene and methacrolein with ozone was investigated at different stages in the condensed phase at temperatures from 15 to 265 K by IR spectroscopy. The results revealed the following overall reaction process: the generation of primary ozonide (POZ), then its decomposition, and finally conversion into secondary ozonide (SOZ), which supported the Criegee mechanism. In the POZ and SOZ of isoprene, ozone cyclo-added preferentially to the double-bond that is not substituted by the methyl group. For methacrolein, the mainly detected SOZ is claimed to be MACSII formed by recombination of the intermediate CH2OO radical with aldehyde carbonyl of methylglyoxal in stead of the ketone carbonyl group. Theoretical calculations were performed at the B3LYP//MP2/6-311++G (2d, 2p) level to analyze the resulting spectrum. The good agreement between the calculated infrared spectra of POZ and SOZ and the experimental spectra supports the above-described findings.