This study proposed an effective signal processing system based on Ensemble Empirical Mode Decomposition (EEMD) method for the analysis of arterial blood pressure (ABP). The whole system was implemented on an ARM-based SoC development platform to attain the on-line non-stationary signal processing. A non-invasive blood pressure acquisition device (NIBP100D) was used to record the continuous ABP as the input signal. According to the non-stationary characteristics of ABP, EEMD is useful to achieve accurate decomposition for ABP spectral analysis. The signal was decomposed into several Intrinsic Mode Functions (IMFs) by EEMD, and quantitatively assessed by fast Fourier transform (FFT). The results showed that the proposed EEMD processor can effectively solve the mode mixing problem of Empirical Mode Decomposition (EMD) and the FFT spectrum of IMF5, IMF6, and IMF7 to reveal heart rate and respiration.