A biological light measuring instrument for illuminating a subject with a plurality of beams of light from a plurality of illuminating positions, measuring the light beams transmitted through the subject, and creating a topographic image showing ecological information about the inside of the subject, comprising unit for creating three-dimensional coordinate data representing the relationship among the illuminating positions and a reference point on the subject and the relationship between the light measuring position and the reference point, unit for setting the illuminating positions and light measuring position on a three-dimensional shape image of the subject according to the three-dimensional coordinate data, and unit for creating a three-dimensional topographic image according to the three-dimensional coordinate data, and unit for superposing the three-dimensional topographic image on the shape image while maintaining the relationships of the illuminating positions and the light measuring position.