A method for treating a substrate using a substrate treating apparatus that includes a treating module and an index module that transfers the substrate between a container and the treating module, in which a plurality of process chambers and a main transfer robot are provided in the treating module and a container mounting table and an index robot that transfers the substrate between the container and the treating module are provided in the index module, includes executing a power failure after-treatment operation and thereafter stopping an operation of the substrate treating apparatus when a power failure occurs in the substrate treating apparatus. When the main transfer robot or the index robot is transferring the substrate in the event of the power failure, the power failure after-treatment operation includes an operation of continually maintaining the transfer of the main transfer robot or the index robot until the transfer is completed.