This paper has presented a photoplethysmography (PPG) signal processing system based on ensemble empirical mode decomposition (EEMD) method. Traditionally, empirical mode decomposition (EMD) suffers from mode mixing problem during the decomposition process. This paper adopts EEMD to solve the mode mixing problem by adding different sets of white noise and decompose signal into meaningful intrinsic mode functions. The system is implemented on self-designed platform combined with front-end circuit, EEMD chip by TSMC 90nm CMOS technology, and commercial display devices. The results showed that the proposed EEMD processor can effectively solve the mode mixing problem of EMD. It was helpful for non-stationary biomedical signal processing and cardiovascular diseases research.