According to one embodiment, deposition supporting system, depositing apparatus and manufacturing method of a semiconductor device includes a depositing apparatus that deposits stacked bodies on wafers allocated to stations and a host computer. The host computer evaluates feature amounts convertible to misalignments at predetermined points on the stacked bodies of the respective wafers, and specifies the stations to which the wafers are to be allocated based on the feature amounts of the stacked bodies in the respective stations. The depositing apparatus allocates the wafers to the stations based on the specification from the host computer.