In a batch type vertical heat-treating method, first, product wafers and dummy wafers are set to be stacked on an upstream side of a flow of a process gas, in heat treatment, within main holding positions of a holder. The dummy substrates are set more downstream of the process gas than the product wafers. The product wafers and the dummy wafers are set in the holder in a total number smaller than a total number of the main holding positions corresponding to a maximum number of wafers that can be held by the holder, and the holder is in a partially loaded state. The partially loaded holder is loaded in a process vessel, and the product wafers are processed in the process vessel.