Spatial light modulator (SLM) is a kind of optical modulating elements for the optical field distribution. It is widely used in optical information processing, beam transformation, output display and many other application fields. With the wide applications of high-resolution SLMs, the microscopic imaging resolution and contrast of phase and amplitude samples are enhanced greatly, which can not only achieve traditional phase microscopic techniques，but also achieve new type microscopic imaging with a more complicated way and flexibility to modulate phase. In microscopy SLM can not only be used to control the sample illumination, but also act as spatial Fourier filters in the imaging path. Some of these flexible applications are reviewed in this article.