The invention discloses a light source system for a bacterial colony counter, a counter and a counting method. The light source system for the bacterial colony counter comprises an upper part light source and a lower part light source located under the upper part light source; the upper part light source comprises a first shell, a first ring light source and a first soft light plate; and the lowerpart light source comprises a second shell, a second ring light source and a second soft light plate. According to the light source system, by arranging the upper part light source and the lower partlight source, a bacterial colony culture container is irradiated for suitable light compensation to the bacterial colony culture container, light compensation includes light intensities and light colors, so that a bacterial colony contour on a collected image is clearer, and has better contrast with substrates around the bacterial colony culture container; and clarity and contrast of a bacterialcolony counter image are improved, so that more accurate bacterial colony data are obtained when statistical software is used for bacterial colony counting, and the light source system is widely usedin the field of environmental biological monitoring equipment.