Provided is an apparatus, system and method for treating a substrate, and more particularly, a substrate treating apparatus having a cluster structure, a substrate treating system, and a substrate treating method using the substrate treating system. The substrate treating apparatus includes a load port on which a container containing a substrate is installed, a plurality of process modules treating the substrate, a transfer module disposed between the load port and the process modules, and transferring the substrate between the container and the process modules, and a buffer chamber disposed between neighboring ones of the process modules, and providing a space for carrying the substrate between the neighboring process modules.