Voriconazole (VRZ) is widely used to prevent and treat invasive fungal infections; however, there are a few studies examining the variability and influencing the factors of VRZ plasma concentrations across different clinical departments. This study aimed to evaluate distinction of VRZ concentrations in different clinical departments and provide a reference for its reasonable use. From 1 May 2014 to 31 December 2020, VRZ standard rates and factors affecting the VRZ trough concentration were analyzed, and a multiple linear regression model was constructed. The standard rates of VRZ in most departments were above 60%. A total of 676 patients with 1212 VRZ trough concentrations using a dosing regimen of 200 mg q12h from seven departments were enrolled in the correlation analysis. The concentration distribution varied significantly among different departments (p < 0.001). Fifteen factors, including department, CYP2C19 phenotype, and gender, correlated with VRZ concentration. A multiple linear regression model was established as follows: VRZ trough concentration = 5.195 + 0.049 × age + 0.007 × alanine aminotransferase + 0.010 × total bilirubin − 0.100 × albumin − 0.004 × gamma-glutamyl transferase. According to these indexes, we can predict possible changes in VRZ trough concentration and adjust its dosage precisely and individually.