Field-effect transistor (FET) biosensors based on two-dimensional (2D) materials have gained extensive attention due to their high sensitivity, label-free detection capability, and fast response. Molybdenum disulfide (MoS2), with tunable bandgap, high surface-to-volume ratio, and smooth surface without dangling bonds, is a promising material for FET biosensors. Previous reports have demonstrated the fabrication of MoS2-FET biosensors and their high sensitivity detection of proteins. However, most prior research has focused on the realization of MoS2-FETs for detecting different kinds of proteins or molecules, while comprehensive analysis of the sensing mechanism and dominant device factors of MoS2-FETs in response to proteins is yet to investigate. In this study, we first fabricated MoS2-FET biosensor and detected different types of proteins (immunoglobulin G (IgG), β-actin, and prostate-specific antigen (PSA)). Secondly, we built the model of the device and analyzed the sensing mechanism of MoS2-FETs in response to proteins. Experimental and modeling results showed that the induced doping effect and gating effect caused by the target protein binding to the device surface were the major influential factors. Specifically, the channel doping concentration and gate voltage (Vg) offset exhibited monotonic change as the concentration of the protein solution increases. For example, the channel doping concentration increased up to ~37.9% and the Vg offset was ~ -1.3 V with 10−7 µg/µL IgG. The change was less affected by the device size. We also investigated the effects of proteins with opposite acid-base properties (β-actin and PSA) to IgG on the device sensing mechanism. β-actin and PSA exhibited behavior opposite to that of IgG. Additionally, we studied the response behavior of MoS2-FETs with different dimensions and dielectric materials (channel length, MoS2 thickness, dielectric layer thickness, dielectric layer material) to proteins. The underlying mechanisms were discussed in details. This study provides valuable guidelines for the design and application of MoS2-FET biosensors.