Abstract: A new architecture of digital control system (DCS) was designed, which could be used in both quadrupole mass filter and quadrupole ion trap mass spectrometer. The architecture was based those of commercial instrument Polaris Q, but added the PC104 bus to extend modules, not use DSP replaced by multi-task programming based uClinux in 32-bit MCU and FPGA, developed the universal remote control protocol, synchronized program based FPGA. The DCS based the new architecture is successfully applied in three product prototypes, which are EI-quadrupole mass filter, EI-rectilinear ion trap and ESI-rectilinear ion trap mass spectrometer. The new architecture can are universality and miniaturization, but DCSs is not satisfy.