Physical inventory is a process of determining that the inventory quantities are exact, or if there are differences in quantity mentioned physically present and that mentioned in the SAP system. Basically, after you are finished with physical inventory, your system and physical stock levels must be the same.
It is mandatory for legal reasons, and in the most of the times it is conducted once a year.
To simplify the process, check the below diagram, these are the most common steps for doing physical inventory (not only in SAP ERP)