A data processing system and a data processing method are capable of separating application processes. The data processing system of the invention includes a data storage device and at least one processor. When a user operates the at least one processor to execute an application process to access a designated file from the data storage device through a file control module residing in a kernel mode of an operating system, the file control module compares a user account of the user and M rules and M characteristics of the application process with a plurality of execution space setting data previously stored to obtain an authority data, where M is a natural number. The file control module selectively returns the designated file to the application process in accordance with the authority data.