Self-interference incoherent digital holography (SIDH) technique allows to capture the complex wavefront information with incoherent light. We suggest a distortion compensation method in an incoherent microscope system using SIDH. To correct the distorted wavefront, we detect the distorted wavefront of a guide-star with SIDH method and modulate the wavefront with a phase-only spatial light modulator (SLM). We present an iterative algorithm that calculates the SLM modulation pattern to correct the wavefront. By the correction, the size of focused spot becomes smaller. It means that the resolution of the image can be improved or even an object covered with a thick aberration layer can be detectable. We verify the feasibility of the wavefront correction method with the simulation and experimental results.