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Tritium is a water-soluble hydrogen isotope that releases beta rays during decay. In nature, tritium primarily exists as tritiated water (HTO), and its main source is nuclear power/processing plants. In recent decades, with the development of nuclear power industry, it is necessary to evaluate the impact of tritium on organisms. In this study, fertilized zebrafish embryos are treated with different HTO concentrations (3.7 × 103 Bq/ml, 3.7 × 104 Bq/ml, 3.7 × 105 Bq/ml). After treatment with HTO, the zebrafish embryos developed without evident morphological changes. Nevertheless, the heart rate increased and locomotor activity decreased significantly. In addition, RNA-sequencing shows that HTO can affect gene expressions. The differentially expressed genes are enriched through many physiological processes and intracellular signaling pathways, including cardiac, cardiovascular, and nervous system development and the metabolism of xenobiotics by cytochrome P450. Moreover, the concentrations of thyroid hormones in the zebrafish decrease and the expression of thyroid hormone-related genes is disordered after HTO treatment. Our results suggest that exposure to HTO may affect the physiology and behaviors of zebrafish through physiological processes and intracellular signaling pathways and provide a theoretical basis for ecological risk assessment of tritium.