Recently, lincomycin has been detected frequently in aquatic environment, especially in the effluent of pharmaceutical wastewater treatment plants. Public concerns have been raised due to its adverse bio-effect and potential of inducing resistance genes. In this study, hydrothermal treatment (HT) was applied to remove lincomycin from high-concentrated pharmaceutical waste water. Influence factors (e.g., temperature, initial concentration and pH) were investigated from kinetics perspective. Meanwhile, degradation byproducts were identified using liquid chromatography-mass spectrometry (LC-MS), based on that transformation pathways were proposed. Finally, the toxicity of lincomycin degradation intermediates were evaluated by Microcystis cells. The results showed that lincomycin was eliminated efficiently via HT and an obvious lag time existed in its degradation process. An autocatalytic model was developed successfully based on the degradation kinetics analysis. The model showed good fitness with experiments data (R-2 > 0.99). Observed reaction constant (k) increased when reaction temperature varied from 110 to 160 degrees C; it decreased from 0.034 to 0.015 min(-1) as pH ranged from 2.0 to 6.0. Additionally, increasing initial concentration of lincomycin promoted its degradation, while it showed a different trend once the concentration exceeded 300 mg L-1. A total of 7 major intermediates were identified, based on which hydrolysis, hydroxylation and desulfuration were inferred as the mainly evolution processes. Finally, toxicity evaluation indicated that both lincomycin and its degradation byproducts have no inhibition on algal strains. Thus, it is concluded that HT is an efficient method for removing lincomycin.