Today, more and more people are caring about their health, so biomedical research is much more important for human being. Biomedical signal processing is one of the most important research areas in biomedical engineering, but most of the biomedical signals are nonlinear and non-stationary signals. And the traditional methods like Fourier transform are limited to the priori assumption that the signals being processed should be linear and stationary, which is a restriction for biomedical signal processing. In 1998, N. E. Huang proposed a novel algorithm which named Hilbert Huang Transform, this algorithm is very good at processing nonlinear and non-stationary signals, and it already has a lot of applications on biomedical engineering. But the huge computation cost is a bottleneck to implement those applications with real-time processing. This thesis presents a “Fast Instantaneous Frequency Analyzer Based on Hilbert transform”, the system can analyze nonlinear and non-stationary signals such as biomedical signals in time-frequency domain with a 3D spectrum. It clearly demonstrates the process of nonlinear and non-stationary signal during changing. And this thesis also proposes a method to use the concept of System On Programmable Chip to combine the soft-core processor with hardware functions to implement the acceleration for Hilbert Huang Transform. After evaluation, this method is proved to be effective.