Most of the materials in nature have complex refractive indexes, especially for biological tissues. The real and imaginary components of the complex refractive index are respectively responsible for the phase delay and absorption of light traveled in the tissues. Taking the complex refractive index into consideration, we modified the imaging theory of phase contrast microscopy. A relationship between the distributions of complex refractive index in measured samples and the intensity distributions of phase contrast micrographs is obtained. Based on this relationship, the influences of the refractive index and thickness of biological slices on the image contrast of phase contrast micrographs are analyzed in detail.