A time-saving method was applied to synthesize methyltrimethoxy-modified magnetic mesoporous silica with or without p-toluenesulfonic acid as the catalyst for magnetic solid-phase extraction. The synthesized materials were systematically characterized. Results demonstrated that methyltrimethoxy modified magnetic mesoporous silica with p-toluenesulfonic acid as the catalyst has a relatively smaller aperture and extreme hydrophobicity (water contact angle of 135°). To evaluate the feasibility of these prepared materials as effective adsorbents, it was combined with gas chromatography and electron capture detection to determine 26 polychlorinated biphenyls in environmental water. The result revealed that methyltrimethoxy modified magnetic mesoporous silica with p-toluenesulfonic acid as the catalyst had the best extraction efficiency and recovery. Under the optimized extracted conditions, the proposed method showed good linearity within the concentration range of 5 to 200 ng/L with correlation coefficients of 0.9969 to 0.9999. The limits of detection and quantification based on signal-to-noise ratios of 3 and 10 were in the range of 0.16 to 0.91 and 0.52 to 3.0 ng/L, respectively. The polychlorinated biphenyl concentrations in environmental water samples were successfully determined using the developed method. PCB008 and PCB110 were 4.05 and 8.52 ng/L in Red-Star lake water (Hubei Province, China), respectively.