Disclosed are a system for pretreatment of sample and a method for controlling the same. The system for pretreatment of sample, including: a holder storage unit having a module holder on which a sample pretreatment module is seated; a cartridge accommodating portion for loading a cartridge therein, wherein the sample accommodated in a chamber of the sample pretreatment module is discharged and loaded into the cartridge; a magnetic force generating unit for generating a magnetic force to rotate the permanent magnet provided in the sample pretreatment module; and a penetration and discharge unit for penetrating the penetration membrane in the sample pretreatment module and discharging the sample by pressing the moving unit of the cap.