As a finite-energy-bandgap alternative to graphene, semiconducting molybdenum disulfide (MoS2) has recently attracted extensive interest for energy and sensor applications. In particular for broad-spectral photodetectors, multilayer MoS2 is more appealing than its monolayer counterpart. However, little is understood regarding the physics underlying the photoresponse of multilayer MoS2. Here, we employ scanning photocurrent microscopy to identify the nature of photocurrent generated in multilayer MoS2 transistors. The generation and transport of photocurrent in multilayer MoS2 are found to differ from those in other low-dimensional materials that only contribute with either photovoltaic effect (PVE) or photothermoelectric effect (PTE). In multilayer MoS2, the PVE at the MoS2-metal interface dominates in the accumulation regime whereas the hot-carrier-assisted PTE prevails in the depletion regime. Besides, the anomalously large Seebeck coefficient observed in multilayer MoS2, which has also been reported by others, is caused by hot photo-excited carriers that are not in thermal equilibrium with the MoS2 lattice.