The influence of the built environment on human health and comfort has become a focal point in contemporary biomechanics research. This study integrates Building Information Modeling (BIM) with numerical simulations and experimental analyses to examine the effects of key environmental factors—vibration, heat stress, and air quality—on human biomechanical responses. An advanced bi-directional progressive optimization algorithm, coupled with biomechanical modeling, was applied to optimize material distribution, load transfer, and human–building interactions. The introduction of a penalty factor P within the optimization framework effectively regulated structural stiffness and attenuated mechanical vibrations transmitted to joints and bones. BIM-based heat flow and surface temperature simulations demonstrated that indoor temperatures above 30 ◦C significantly increased cardiovascular and thermoregulatory strain, particularly in elderly individuals and children. The optimized designs reduced the heat stress index (HSI) by 18.7%. Vibration environment optimization further revealed that tailored adjustments to building materials and structural configurations decreased joint and spinal stress, resulting in an 18% reduction in physiological responses among the elderly and a 12% decrease in vibration perception among children.