In this paper, a new calibration method for a specially designed photometric stereo system was presented. Different from conventional photometric stereo systems which adopt parallel or distant point light sources, the quasi-point light sources are used in the proposed system, which permits the system with compact size and short working distance. Subject to the non-isotropic radiance property of the quasi-point light source, the lighting field should be precisely calibrated so as to determine the intensity and direction for each incident light ray. The proposed calibration method was performed in two steps. The first step was to calculate light source position, where a multi-sphere-based method was introduced. By extracting the highlight image points formed from the light source on the specular sphere, and utilizing the sphere contour and radius, it shows that the light source coordinate under camera reference frame can be precisely estimated. In second step, a reference plane-based method was proposed to calculate the principle optical axis of light source. It proves that, the principle optical axis should cross the brightness point in the image of reference plane, and the brightness point can be estimated by fitting the iso-luminance curve in the image. With the calibration parameters, and considering the radiance model of light source, lighting condition for each scene point can be determined. The experiments were conducted with various target surfaces and compared with conventional light models to demonstrate feasibility and accuracy improvement by the proposed calibration method.