The shipping industry faces urgent pressure to decarbonize in response to tightening regulations and growing concerns over marine pollution. Computational Fluid Dynamics (CFD) has emerged as a pivotal technology, enabling a paradigm shift from empirical design to precision-driven optimization for energy efficiency. This systematic review critically evaluates CFD applications across key domains: hull form optimization, surface drag reduction, propulsion improvements, wind-assisted propulsion integration, engine emission abatement, and operational management strategies. Analysis quantifies CFD-driven impacts: hull optimization consistently achieves 5%-12% resistance reduction; surface technologies yield up to 10%-30% drag reduction; propeller and wake field improvements contribute 2-10% propulsive efficiency gains. Collectively, these advancements enable an integrated hull-propulsion-operation framework that delivers substantial lifecycle emission reductions. However, challenges persist in accurately modeling multi-physics coupling and achieving holistic system-level co-design, necessitating vessel-specific solutions and standardized energy efficiency assessment frameworks. Future research should synergize AI with CFD for accelerated surrogate-based optimization, employ digital twins for real-time lifecycle performance management, and advance zero-carbon fuel propulsion systems. This review outlines a CFD-informed pathway for shipping's sustainable decarbonization, highlighting both achieved impacts and emerging opportunities.