The invention provides a water seismic refractive data acquisition method based on a bubble seismic source and belongs to the field of engineering investigation. A green, environment-friendly, high-efficiency, low-cost, safe and reliable bubble seismic source replaces an explosive seismic source so as to excite seismic waves in river water under the condition that the target exploration depth is guaranteed, a reciprocity principle is adopted, and external data acquisition is performed in a mode of receiving signals on both sides of the river. The method comprises the following steps: acquiring river-across profile water seismic refractive wave data by adopting a meeting time distance curve observation system; conveying a bubble seismic source to excitation points so as to excite the seismic waves point by point according to a certain distance by using a measuring line arranged on the ship edge in advance; and receiving the seismic waves at the ends of the measuring lines on both sides of the river by using a digital detector so as to finish the data acquisition. The method is successfully applied to domestic and overseas water-power engineering, achieves an excellent effect and is high in practicality. The data acquisition and operation mode of the traditional water seismic refractive exploration is changed, and the method has wide market prospects and popularization values in hydroelectric exploration on water.