The Baishizhang (BSZ) deposit is a newly discovered large-scale Mo(W) deposit in the Nanling Range, South China. Scheelite occurs both as intergrown with molybdenite (Sch
I) and individually (Sch
II), making it a key mineral for understanding molybdenum exploration at the BSZ deposit. We present trace element and Sr isotope data for SchI and SchII from the BSZ deposit to elucidate the precipitation mechanisms and fluid sources of the mineralization. Our data reveal that the geochemical composition of SchI and SchII exhibit at first order numerous similarities, and the substitution mechanism is the first order physico-chemical parameter controlling the composition of scheelite, with 3
ACa
2+ = 2
A(REE, Y)
3+ + Ca
vac (Cavac = Ca site vacancy) being the dominant mechanism for REE and Y incorporation into the Ca-site of scheelites in the BSZ deposit. This means that the REE distributions of the scheelite in this study could record features of mineralizing fluids. The low Mo, As, and V contents in the BSZ scheelites indicate a reducing environment during mineralization. The Y/Ho values (SchI: mainly 9.71–57.96 and SchII: mainly 14.70–58.85) and
87Sr/
86Sr ratios (SchI: 0.737970–0.740379; SchII: 0.733081–0.736318) imply mixed hydrothermal fluid sources. The geochemical signatures (
87Sr/
86Sr ratios and trace element composition) of scheelites, compared with those of associated granites and country rocks, suggest that the mineralizing fluids were primarily derived from deep concealed granites but were also significantly modified by interaction with country rocks. The second order compositional variations between SchI and SchII are mainly controlled by the composition of mineralized fluids. The orthogonal partial least squares-discriminant analysis (OPLS-DA) results indicate that the most significant elemental differences between Sch
I and Sch
II are Y, Nb, and REE. Collectively, we can utilize the distinct elemental differences among scheelite in the BSZ deposit to fingerprint the characteristics of molybdenum mineralization.