In view of the disadvantages of the traditional ionospheric oblique sounder like complex structure, the fixed sounding path, and the serious coherent interference among multiple stations, a detection method for the embedded ionospheric oblique sounding system based on the Field Programmable Gate Array(FPGA) and Advanced Reduced Instruction Set Computing Machines(ARM) is proposed, and the design of system structure is put forward. Firstly, the complete complementary code is adopted to solve the problem of coherent interference in simultaneous detection of multiple stations. Secondly, the digital intermediate frequency receiving structure is used for secondary mixing in the digital domain, avoiding spurious signals and intermodulation distortion, bearing the characteristics of standardization, modularization and good expansibility. The Flexible Static Memory Controller(FSMC) protocol provides a high-speed parallel data transmission method between control modules. Finally, the data automatic judgment and optimal frequency selection are realized. The experimental results verify the correctness and reliability of the design. It has important application prospects in space physics, sky-wave over-the-horizon radar detection, emergency rescue and disaster relief and other fields.