Abstract: Disclosed are a method and a system for comprehensive evaluation of organic compound and heavy metal pollution in water based on fish electro-cardio, and fish electro-cardio signals are acquired by a real-time and miniaturized fish electro-cardio acquisition system which includes a real-time and miniaturized fish electro-cardio acquisition device, then a change of the electro-cardio index in a QT interval is obtained for assessing the corresponding organic compound in water to be tested, and a change of the electro-cardio index in a QRS interval is obtained for assessing the corresponding heavy metal in water to be tested. Based on fish electro-cardio acquired continuously on-line in real-time while keeping fish swims in a normal state and the water quality parameters acquired by various water quality sensors, water quality is online analyzed and water sudden pollution is online monitored and assessed.