Facile and sensitive methods for detecting neonicotinoids (NEOs) in aquatic environments are crucial because they are found in extremely low concentrations in complex matrices. Herein, nitrogen-based magnetic conjugated microporous polymers (Fe3O4@N-CMP) with quaternary ammonium groups were synthesized for efficient magnetic solid-phase extraction (MSPE) of NEOs from tap water, rainwater, and lake water. Fe3O4@N-CMP possessed a suitable specific surface area, extended π-conjugated system, and numerous cationic groups. These properties endow Fe3O4@N-CMP with superior extraction efficiency toward NEOs. The excellent adsorption capacity of Fe3O4@N-CMP toward NEOs was attributed to its π–π stacking, Lewis acid–base, and electrostatic interactions. The proposed MSPE-HPLC-DAD approach based on Fe3O4@N-CMP exhibited a wide linear range (0.1–200 µg/L), low detection limits (0.3–0.5 µg/L), satisfactory precision, and acceptable reproducibility under optimal conditions. In addition, the established method was effectively utilized for the analysis of NEOs in tap water, rainwater, and lake water. Excellent recoveries of NEOs at three spiked levels were in the range of 70.4 to 122.7%, with RSDs less than 10%. This study provides a reliable pretreatment method for monitoring NEOs in environmental water samples.