Empirical Mode Decomposition (EMD) can analyze non-stationary signal in time-frequency domain accurately, and be used widely. Virtual Instruments has made a very fast development, with the help of powerful modular hardware, combined efficient and flexible software, graphical LabVIEW language can meet all the needs of test, measurement and automation, and can improve efficiency widely. In this paper, LabVIEW is be used to design the program of Hilbert Huang Transform (HHT), by analyzing EMD and instantaneous frequency, and has been proved by simulation that the program can run effectively. The program provides more choices for LabVIEW signal processing module.