The invention discloses a microwave thermoacoustic, optical acoustic and ultrasonic three-modal intestinal tissue imaging method and system, and relates to a medical imaging technology. The microwavethermoacoustic, optical acoustic and ultrasonic three-modal intestinal tissue imaging method comprises the steps that intestinal tissue ultrasonic images are obtained, a pulse laser and a pulse microwave are emitted to a to-be-imaged area of intestinal tissue, thus intestinal tissue optical acoustic signals and intestinal tissue thermoacoustic signals are generated in the to-be-imaged area of theintestinal tissue and converted into electrical signals, through amplification, filtering, A/D conversion and image reconstruction, intestinal tissue optical acoustic images and intestinal tissue thermoacoustic images are obtained, and the intestinal tissue optical acoustic images subjected to color coding and the intestinal tissue thermoacoustic images subjected to color coding are superimposed on intestinal tissue ultrasonic images. The microwave thermoacoustic, optical acoustic and ultrasonic three-modal intestinal tissue imaging system comprises an ultrasonic imaging module, a pulsed laser, a pulse microwave source, a ultrasonic transducer, a signal processing unit, a data collecting unit and a computer. The imaging method is a non-invasive method, operation is convenient, patients donot have pain, and imaging of the intestinal tissue can be realized more comprehensively.