Natural organic matter (NOM) in aquatic environments have a significant impact on NOM-organic compound interactions, which could strongly affect the distribution and transformation of organic compounds during water treatment. This study focused on the removals of NOM (humic acid, HA) and synthetic organic matter (ibuprofen, IBP) through enhanced coagulation and magnetic ion exchange (MIEX) resin adsorption in single and bi-component systems. Two coagulants, traditional aluminum sulfate (AS) and lab-prepared polyaluminum chloride (PACl), were employed. The charge properties, particle size distribution, and fractal dimension (Df) during organic matter removal were studied in both the single and bi-component systems to explore the purification behaviors and mechanistic effects of interactions between coagulants, MIEX, and organic matters. The experimental results indicated that the Al-based coagulants could remove over 80% of HA in both the single and IBP-HA combined systems, while the presence of HA could considerably improve the IBP removal rate. The aggregates formed during single-component coagulation were larger, but weaker and more loosely structured than those formed in the bi-component system under the same coagulation conditions. In the single-component system, the maximum removal efficiencies of IBP and HA by MIEX adsorption were 65% and 72%, respectively, at a resin dosage of 20.0 mL/L and mixing time of 60 min. Under the same conditions, the removals of these components in the bi-component system were improved to 68% and 98%, respectively. The reaction rate between IBP and MIEX resin was found faster than that between HA and MIEX resin.