Kashin-Beck Disease (KBD), an osteoarticular disorder, is potentially influenced by several factors, among which selenium deficiency and HT-2 mycotoxin exposure are considered significant. However, the combined effect of these factors on femoral development remains unclear, Conducted over eight weeks on forty-eight male mice categorized into control, selenium-deficient, and HT-2 toxin-exposed groups, including dual-exposure sets, this study comprehensively monitored body weight, bone metabolism markers, and cellular health. Employing biomechanical analysis, micro-computed tomography (micro-CT), and transmission electron microscopy (TEM), we unearthed a reduction in body weight due to HT-2 toxin alone, with selenium deficiency exacerbating these effects synergistically. Our results unveil that both factors independently affect bone metabolism, yet their confluence leads to a pronounced degradation of bone health parameters, including alterations in calcium, phosphorus, and vitamin D levels, alongside marked changes in osteoblast and osteoclast activity and bone cell structures. The notable damage to femoral cortical and trabecular architectures underscores the perilous interplay between dietary selenium absence and HT-2 toxin presence, necessitating a deeper understanding of their separate and joint effects on bone integrity. These discoveries underscore the imperative for a nuanced approach to toxicology research and public health policy, highlighting the pivotal influence of environmental and nutritional factors on skeletal well-being.