Herein, we demonstrate the ability of a dual-purpose periodic mesoporous organosilica (PMO) probe to track the complex chlorinated paraffin (CP) composition in living animals by assembling it as an adsorbent-assisted atmospheric pressure chemical ionization Fourier-transform ion cyclotron resonance mass spectrometry (APCI-FT-ICR-MS) platform and synchronously performing it as the in vivo sampling device. First, synchronous solvent-free ionization and in-source thermal desorption of CP homologues were achieved by the introduction of the PMO adsorbent-assisted APCI module, generating exclusive adduct ions ([M − H] − ) of individual CP homologues (C n Cl m ) with enhanced ionization efficiency. Improved detection limits of short-and medium-chain CPs (0.10−24 and 0.48−5.0 pg/μL) were achieved versus those of the chloride-anion attachment APCI-MS methods. Second, the dual-purpose PMO probe was applied to extract the complex CP compositions in living animals, following APCI-FT-ICR-MS analysis. A modified pattern-deconvolution algorithm coupled with the sampling-rate calibration method was used for the quantification of CPs in living fish. In vivo quantification of a tilapia exposed to technical CPs for 7 days was successfully achieved, with ∑SCCPs and ∑MCCPs of the sampled fish calculated to be 1108 ± 289 and 831 ± 266 μg/kg, respectively. Meanwhile, 58 potential CP metabolites were identified in living fish for the first time during in vivo sampling of CPs, a capacity that could provide an important tool for future study regarding its expected risks to humans and its environmental fate.