Objective: To monitor total trough concentration (C min_total ) and unbound trough concentration (C min_free ) of vancomycin in clinical samples and analyze the factors influencing them, and to assess their correlation with clinical efficacy and acute kidney injury (AKI). Methods: Plasma samples were processed by protein precipitation, followed by hollow-fiber centrifugal ultrafiltration to separate unbound vancomycin from plasma. Thereafter, C min_total and C min_free were determined using high-performance liquid chromatography. Clinical data of patients were collected. Factors affecting vancomycin C min_total , C min_free , and their correlation with clinical efficacy and nephrotoxicity were investigated. Results: A total of 146 samples from 105 included patients were collected. C min_total and C min_free of vancomycin ranged from 0.62 to 56.08 mcg·mL −1 and 0.61–38.51 mcg·mL −1 , respectively. C min_total and C min_free were correlated (r = 0.8899), influenced by basal creatinine and cystatin C. Higher level of C min_free (˃8.6 mcg·mL −1 ) and nephrotoxic drugs concomitant were risk factors of vancomycin-associated AKI ( P < 0.05); C min_total and C min_free thresholds of vancomycin-associated AKI were 15.35 and 6.83 mcg·mL −1 , respectively. Conclusions: vancomycin C min_total and C min_free , higher C min_total and C min_free were correlated and higher concentrations of both may increase the risk of AKI.