The removal capacity of aftertreatment technologies equipped on diesel exhaust in intermediate and semivolatile organic compounds (I/SVOCs) remains unclear. This study quantified the effect of typical aftertreatment technologies (China VI) on diesel engine-emitted I/SVOCs, related secondary organic aerosol (SOA), and toxic effects. The equipped aftertreatment devices could mitigate the emission factors (EFs) by 70.8 ± 3.4 to 82.5 ± 20.9% for I/SVOCs, 72.7 ± 18.6 to 77.5 ± 4.2% for SOA production, and 75.7 ± 9.3 to 82.4 ± 9.2% for toxic equivalent quantity (TEQ). Aftertreatment units are better for removing alkanes, benzenes, and ketones. The TEQ from the cold-start cycle is 1.3-to 5.7-fold higher than that from the hot-start cycle. In contrast, the EFs of ship-emitted I/SVOCs are 3.7-to 5.3-fold higher than those of diesel vehicles equipped with an aftertreatment system when burning the same fuel, leading to 2.1-to 3.0-fold higher SOA production and 3.1-to 6.7-fold TEQ. Implementation of control devices on marine diesel engines could reduce I/SVOC EFs, SOA production, and eye irritation TEQ of ships by 76.7 ± 12.2, 75.1 ± 12.2, and 79.1 ± 9.6%, respectively. These results indicate that it is vital to equip marine engines with aftertreatment technologies to improve air quality and protect human health.