Herein, we developed a unique fluorescence biosensor for methotrexate assay based on MoS2 quantum dots, which were synthesized in one step using sodium molybdate and cysteine as raw materials. The fluorescence of MoS2 QDs could be quenched when encountered with methotrexate, which was attributed to the inner filter effect (IFE). Furthermore, this present IFE-based method showed the linearity between the MoS2 QDs fluorescence intensity and the methotrexate concentration in the range of 0.05-1 μM with the LOD of 42 nM. The practical applicability of this strategy was successfully demonstrated by detecting methotrexate in real samples. Results indicated that the proposed method could be a promising sensing platform for methotrexate analysis.