A data processing apparatus and a data processing method thereof for an Internet of Things (IoT) system are provided. The data processing apparatus generates a plurality of diagnosis rule data, diagnoses each of the device data received from at least one IoT apparatus to generate a plurality of diagnosis log data, packages the device data, the diagnosis log data and the diagnosis rule data respectively based on a preset data amount to generate a plurality of device files, a plurality of diagnosis log files and a plurality of diagnosis rule files individually, stores each device file, each diagnosis log file and each diagnosis rule file in an interplanetary file system individually, and stores hash values of each device file, each diagnosis log file and each diagnosis rule file in a blockchain system individually.