Confined enzyme catalysis is a promising approach for pharmaceutical synthesis because it can combine high selectivity, catalytic efficiency and mild reaction conditions. This review examines recent advances in multiscale enzyme confinement for pharmaceutical applications, with emphasis on atomic-scale active-site regulation, molecular-scale immobilization and transport control and multi-enzyme cascade organization. We discuss how confined microenvironments modulate enzyme electronic states, conformational dynamics, substrate accessibility, local reaction conditions and intermediate transfer, thereby influencing catalytic activity, stability and stereoselectivity. Representative applications across major enzyme classes are discussed, with a focus on the synthesis of chiral drug intermediates and complex pharmaceutical molecules. The review also considers process-level sustainability, including process mass intensity (PMI) and the E-factor, together with limitations related to mass transfer, support preparation, long-term stability, scale-up and support material burdens. Overall, integrating multiscale confinement with spatially organized cascade catalysis offers a promising route toward more efficient and potentially more sustainable pharmaceutical manufacturing, although its net environmental benefit must be established through system-level assessment.