The invention discloses a deep inspection system and a method used on a basic software and hardware platform of a large data center IT system. The invention is characterized in that: the deep inspection system comprises an inspection main control module, an inspection object definition table, an inspection item definition table, an inspection item local personalization definition table, a fault scanning module, a security scanning module, a SOX scanning module, a performance scanning module and a data collection module, a License scanning module, and a distribution/deployment/collection module; during the inspection process, a destination range, an inspection item and an inspection item local of the inspection are respectively customized to ensure the destination range, the inspection item and the inspection item local of the inspection first, through the inspection object definition table, the inspection item definition table and the inspection item local personalization definition table; then the scanning is acted, namely, an inspection general control module starts up to control and select one module or a plurality of modules from the fault scanning module, the security scanning module, the SOX scanning module, the performance scanning module and the data collection module, the License scanning module and the distribution/deployment/collection module for inspection; at the same time, the inspection general control module adopts a nesting double-layer cycle to call each function module subroutine to inspect initially, to obtain an initial inspection result; after the double-layer cycle scanning, an initial inspection result file is collected by the inspection general control module and then is processed, filtered and analyzed for a second time, and is output to a result file.