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Exhaust after-treatment (EAT) thermal management remains a critical challenge for diesel engines operating under low-load conditions, where low exhaust temperatures delay catalyst light-off and reduce emission control efficiency. This operating regime is common in marine auxiliary engines and onboard diesel generator sets during hoteling, maneuvering, and partial-electrical-load conditions. Conventional strategies such as late fuel injection or exhaust throttling can increase exhaust temperature but often result in significant fuel consumption penalties. This study numerically investigates the combined use of late exhaust valve opening (LEVO) and cylinder deactivation (CDA) to enhance EAT thermal management with a reduced fuel penalty. A six-cylinder diesel engine is analyzed at a low-load condition (1200 RPM, 2.5 bar BMEP) using a calibrated one-dimensional engine simulation model. LEVO applied to all cylinders increases exhaust temperature to approximately 250 °C, but with a considerable increase in fuel consumption. When two cylinders are deactivated and the remaining cylinders operate with LEVO, airflow and pumping losses decrease, enabling higher exhaust temperatures at comparable fuel consumption levels. Despite a 30% reduction in exhaust mass flow rate, the higher exhaust temperature dominates EAT heat transfer. Consequently, the combined strategy increases EAT heat transfer by up to 143% and achieves exhaust temperatures approaching 295 °C. These results indicate that combined valve timing and load redistribution through CDA can improve the exhaust temperature–mass flow trade-off, providing a potential pathway for enhanced EAT warm-up during low-load operation within the limitations of the numerical model. Full article