The laser irradiation on organism will produce a series of biological effects, which can be used for basic medical research, diagnosis and treatments of diseases. However, the mechanism of this biological effects is still unclear. As a sensitive molecular monitoring technique, Raman spectroscopy has became a very popular detection method in biomedical research especially in vivo study. In this paper, we present a compact and flexible micro-Raman system for in vivo studying the mechanism of laser biological effects. The system has the two functions of laser induction and Raman measurement, which can realize the micro-area radiation of laser and simultaneously collect the corresponding Raman spectra in vivo. The detection method provided by this home-built system is able to deepen the understanding of laser biological effects mechanism at molecular level, so it is expected that the system is significant for the treatments and diagnosis of diseases in the near future.