Surface gastric electromagnetic signal is an important basis for the study of gastrointestinal dynamics. Surface electrode method can only collects the gastric slow wave which is the characterization of gastric contraction rhythm. But it can collect the gastric electrical fast signal which is the characterization of the contraction strength of stomach. Because the fat layer has the filtering effect on gastric electric signal. And the permeability of the fat layer is approximate to 1, the feature of gastric electrical fast wave can be acquired by measuring the gastric magnetic signal. To solve this problem, this paper puts forward a method of using the sensor base on the giant magneto impedance effect (GMI) to measure the gastric magnetic signal. We use GMI sensor, and design a gastric magnetic signal collection system, according to the actual data analysis of the noise sources, and put forward gastric magnetic signal de-noising algorithms based on wavelet analysis and chaos theory to remove the corresponding noise, which provides the basis for the extraction of gastric electrical fast wave signal.