Single-photon ionization mass spectrometry (SPI-MS) is a versatile and powerful analytical technique for online and real-time analysis of organic species; however, it is confronted with an intrinsic drawback of lacking structural information on the investigated molecules, let alone differentiation of isobaric compounds. In this work, we describe a first attempt to integrate in-source collision-induced dissociation (CID) to the SPI ion source in a SPI-MS instrument. The in-source CID was accomplished by elevating the pressure in the ion source to medium vacuum pressure (MVP) and raising the extraction voltage. With the aid of in-source CID, both the SPI-induced molecular ion and CID-generated fragment ion mass spectra can be obtained to endue each analyte with its unique spectrometric "fingerprint". The capability for differentiation of isobaric compounds is demonstrated by analyzing two groups of isobaric compounds with molecular weights of 72 and 106 Da, respectively, and quantitative analysis of p-xylene and ethylbenzene in gas mixture. As a result, isobaric compounds with different characteristic fragment ions or appearance energies can be successfully distinguished. The work presents a feasible method for practical applications of SPI-MS to differentiate isobaric compounds conveniently and rapidly without MS/MS technique or coupling additional separation technologies.