AbstractIn this study, thermosonic sterilization (TS), ultrasonic sterilization (US), and heat sterilization at 60°C, 80°C, and 90°C were used for the bactericidal treatment of black carrot juice. The processed samples were analyzed in terms of physicochemical, biological activity, microbial, and metabolomics approaches. The main differential metabolites were identified after treatment. Among these, the content of the important chemical component anthocyanins increased by 10.64% and 6.82% in TS and US, respectively. The TS treatment showed better retention of most of the active substances such as carbohydrates, malic acid, alanine, sterols, lutein, and terpenes compared to the other treatments. Furthermore, the TS treatment reduced the ultrasonic power and time for inactivating microorganisms and increased the DPPH radical scavenging activity by 11.31% compared to the control. The experimental results showed that the black carrot juice after TS treatment with 60% ultrasonic power at 60°C for 5 min sterilization was more favorable for the retention of nutrients and volatiles, improving the quality, safety, and economic potential of black carrot juice.Practical applicationsThis work for the first‐time applied TS to black carrot juice. The effect of TS treatment on the quality of black carrot juice was studied and compared with ultrasonic and conventional heat treatment by metabolomics approach. TS could significantly reduce US treatment time from 25 min (20°C) to 5 min (60°C) for the sterilization of juice. TS has a better effect on the retention of nutrients and flavor substances in the juice. The study is beneficial to the application of TS in purple carrot juice sterilization, also the application of ¹H‐NMR and GC–MS metabolomics approach in food processing.