Abstract: In order to improve the efficiency of auscultation for doctors in screening patients with Congenital Heart Disease (CHD), a heterogeneous real-time PCG and ECG acquisition system based on All Programmable System on Chip(APSoC) is designed. The system realizes the real-time parallel acquisition of visual PCG and ECG signals through the collaborative work of software and hardware. The system is designed with an embedded CPU+FPGA heterogeneous computing architecture and implemented on the APSoC-Zedboard platform. APSoC heterogeneous structure is divided into two programmable parts: PL and PS. The PL part is responsible for receiving the heart sound ECG signal of the acquisition module of the lower computer, and driving the ADV7511 to realize the HDMI high-definition image display. The PS part is responsible for supporting the Linaro operating system to run the Qt Creator program, which realizing the real-time waveform drawing and storage of PCG and ECG signals. The experimental results show that the system is low in cost, small in size, easy to carry and strong in anti-interference ability. It can collect PCG and ECG signals in real-time and parallel conveniently. The system can be used for clinicians to diagnose and screen the children with CHD, and provides support for the subsequent development of portable CHD machine-assisted diagnosis system.