Under the background of high concentration of equity, it has become a normal state that large shareholders have invaded the interests of the company, leading to serious corporate governance problems. Under this circumstance, it is particularly important to explore effective corporate governance mechanisms to curb the tunneling of large shareholders, protect the interests of small and medium shareholders, and improve the quality of the earnings of the listed companies. Based on the perspective of the independent director system in the corporate governance mechanism, this paper uses the sample of small and medium-sized listed companies in China from 2011 to 2015 to discuss whether the reputation of independent directors can effectively suppress the tunneling behavior of large shareholders. The conclusions shows that the reputation of independent directors can inhibit the tunneling behavior of large shareholders. Compared with the reputation of independent directors of academics, the reputation of independent directors of practice inhibiting the tunneling behavior is more significant. The external auditors will issue non-standard audit opinions for tunneling behavior of large shareholders, so it has a certain effect in managing the tunneling of large shareholders.