The designing scheme of a multi output low phase difference agile frequency source has been proposed in this paper. The system schematic diagram, software design and the control flow chart have been presented. The experimental results show that the phase difference of ten path output of PLL & DDS module is less than ±3°, transient time is 17.2 μs, and phase noise is equal to or less than -109 dBc/Hz@1 kHz. The proposed project has the advantages of easy to control, low phase noise, fast hopping and low phase difference between multi output signals; furthermore it has good practicability and expansibility. The design has verified in the practical project and has excellent application effects.