A time-of-flight identification system and method for warehousing and freight transportation are provided by assembling an optical identification device in a container. The optical identification device includes a first, a second, and a third image capturing units, a beam receiving and calibrating unit, an estimation and processing unit, a transmission module and a power supply module. The optical identification device is connected to a monitoring device via signals; wherein the optical identification device is used to perform multi-segment space flight time identification method for logistics managers or inventory personnel to check whether inventory personnel correctly store the goods in storage space inside the container; to improve space utilization rate for the container. The present invention can be installed in: truck container, refrigerated truck container, truck rear cargo container, port centralized container, so as to promote cargo management efficiency and safety.