Tributyltin (TBT), an endocrine disruptor is used globally in agribusiness and industries as biocides, heat stabilizers, and in chemical catalysis. It is known for its deleterious effects on bone by negatively impacting the functions of osteoblasts, osteoclasts and mesenchymal stem cells. However, the impact of TBT on the metabolomics profile in bone is not yet studied. Here, we demonstrate alterations in chemical metabolomics profiles measured by solid state ¹H nuclear magnetic resonance (¹H NMR) spectroscopy in zebrafish bone following tributyltin (TBT) treatment. TBT of 0, 100, 200, 300, 400 and 500 μg/L were exposed to zebrafish. From this, zebrafish bone has subjected for further metabolomics profiling. Samples were measured via one-dimensional (1D) solvent -suppressed and T₂- filtered methods with in vivo zebrafish metabolites. A dose dependent alteration in the metabolomics profile was observed and results indicated a disturbed aminoacid metabolism, TCA cycle, and glycolysis. We found a significant alteration in the levels of glutamate, glutamine, glutathione, trimethylamine N-oxide (TMAO), and other metabolites. This investigation hints us the deleterious effects of TBT on zebrafish bone enabling a comprehensive understanding of metabolomics profile and is expected to play a crucial role in understanding the deleterious effects of various endocrine disruptor on bone.