A substrate treating apparatus includes a process module including a plurality of process units that perform a plurality of steps included in a substrate treating process and that perform the substrate treating process on substrates sequentially placed in the process units based on process recipes for the substrates, a scheduler that controls operations of the process module and the process units included in the process module, a storage that stores transfer paths information of the substrates, and a selection module that selects a process unit to proceed, by a result of feeding back the transfer paths information stored in the storage to the scheduler. The substrate treating apparatus may further include a measuring instrument that measures defect values of the transfer paths information along which the substrates are transferred. The storage may store the defect values measured by the measuring instrument according to the transfer paths information of the substrates.