Hydroxysafflor yellow A (HSYA) is the main water-soluble compound of safflower. It is commonly used in liver disease treatment and has anti-osteoporotic activity. However, the specific mechanism of HSYA is not yet fully understood. Thioacetamide (TAA) has toxic effects on the liver and is widely used in establishing animal models of cirrhosis and liver fibrosis. In research of liver-related diseases and bone deformation in vivo, the zebrafish has become a frequently utilized animal model. In establishing a TAA-induced zebrafish liver injury model, we found that TAA-induced zebrafish also developed osteopenia. The aim of our study is to investigate the protective effect of HSYA on TAA-induced liver injury and osteopenia in zebrafish. The findings demonstrated that HSYA alleviated hepatic oxidative stress, inhibited the release of inflammatory factors, and promoted in vivo skeletal mineralization in zebrafish larvae. Further Real-time Polymerase Chain Reaction and Western blotting analyses showed that HSYA altered the expression levels of SIRT1, HMGB1, TLR4, MYD88 and NF-ΚB, ameliorated TAA-induced liver injury, reduced the release of inflammation-related factors IL-6, IL-1β, TNF-α, regulated the ratio of RANKL/OPG, ameliorated TAA-induced osteopenia. In conclusion, our study demonstrated that HSYA exhibited a noteworthy beneficial influence on TAA-induced liver injury and osteopenia in zebrafish, this finding provide a foundation for the application of HSYA in clinical research.