Compound-specific chlorine isotope analysis (Cl-CSIA), combined with isotopic fingerprinting, is an important method for evaluating the characteristic sources of perchloroethylene (PCE) and exploring the environmental behavior of trace PCE, which is a carcinogen in a contaminated aquifer. By adjusting certain parameters of the instruments, gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS) for PCE with an innovative HP-5 MS column (30 m × 0.25 mm i.d. × 0.14 µm film thickness) was achieved, thereby improving separation efficiency for the Cl-CSIA of PCE. Study results show that the 37Cl/35Cl ratio of PCE (> 99.5%, GCS, Sinopharm Group Co., Ltd.) was stable at different concentrations and reduced the chromatographic peak time to 3.89 min. The separation time was 10% shorter than that in the conventional method. The most accurate 37Cl/35Cl ratio obtained in the molecular ion method was 0.3156 ± 0.0010 at a concentration of 0.0020 µg/mL. The chlorine isotope ratio calculated using the ion fragment method was 0.3207 ± 0.0018. A relatively large error was obtained at 0.05 µg/mL. Samples whose contents were between 1 and 50 µg/mL were sufficient for the achievement of a chlorine isotope ratio precision (σ) of 1‰. Optimal concentrations were determined, and the relative accuracy and stability of the method were verified by two evaluation methods. Therefore, given the high separation efficiency, a large number of mixed samples containing organochlorine contaminants can be tested within a short period, which can reinforce the research on organic contaminants in groundwater.