A paper spray mass spectrometry (PS-MS) method for rapid and reliable analysis of benzalkonium chloride (BAC) in compound eye drops and body surface disinfectant was developed. The sample was dropped onto triangular filter paper, and high voltage (3.5 kV) was applied to form an electrospray. This method can provide the composition of benzalkonium chloride in samples without pretreatment, solvent or chromatographic separation, and the analysis time is only 10 s. The primary homologues C12-BAC, C14-BAC and C16-BAC of benzalkonium chloride were quantitatively analyzed using PS-MS. Samples were subjected to simple dilution and quantified using the internal standard method. Ion trap mass spectrometry was scanned using SIM mode. The linear ranges of C12-BAC, C14-BAC and C16-BAC were 1–100 μg mL−1; the linear regression coefficients were 0.998–0.999; the detection limits (LODs) were 0.1 μg mL−1; the limit of quantifications (LOQs) was <1 μg mL−1, and the method validation indicated that the method precision and accuracy were good. Compared with HPLC-UV methods, there was no significant difference in the quantitative determination of the actual samples, but the analysis time for PS-MS is shorter (2 min). In addition, reagent consumption in PS-MS is small, and no chromatographic separation is needed, suggesting that PS-MS is especially suitable for high-throughput analysis.