Aiming to establish a comprehensive and rapid method to discriminate Onchidium struma（O. struma） quality from different regions, this research has established it’s three extract fingerprints in absolute ethyl alcohol, chloroform and ethyl acetate adoptd the infrared spectrometry (IR), and the information of infrared spectra of O. struma samples originated from 6 regions has been collected. Automatic baseline correction and automatic optimized smoothness of Nicolet 5700 infrared spectrometer intelligence system are applied to optimize the IR fingerprint. Combining with the OPUS software. The results showed that, the three extract fingerprints function as a evaluation index to discriminate O. struma from different regions or different quality. The characteristic absorption peaks of three extracts has been contrasted, reflecting that the IR fingerprint spectra of ethyl acetate extract can reflect more abundant chemical composition information. The three extracts have different level and angle for identification of O. struma. Dual-indexes sequential analysis comparison shows that infrared spectrum of chloroform extract can reflect different habitats and different process mode O. struma differences: It has shown ShangHai（SH）and NingDe（ND）, WenZhou（WZ）and XiaMen（XM）were the region closer samples with higher common peak ratio（≥63.4）and lower variant peak ratio（≤38.5）; Sample SH and YueNan（YN）,YanCheng（YC）and XiaMen（XM）from the farther regions, were significant disparity with lower common peak ratio（≤40.9％）and higher variant peak ratio（≥50.0％）; In addition, sample XM and YN from closer region but have different process mode, which resulted in much lower common peak ratio（38.1％）and much higher variant peak ratio（125.0％）, To sum up, the quality control of aquatic products is a major concern for both the health authorities and the public, considering that current commercially available O. struma are acquired in natural way, acquiring area and time leading to the vital difference of their quality. The method of chloroform extracts dual-index sequence analysis could be used exactly and conveniently in qualitative evaluation of different region samples, and clarified the similarity level among different areas, also applied the quality evaluation of O. struma.