We develop a new auto-guiding system for the Camera for QUasars in the EArly uNiverse (CQUEAN). CQUEAN is an optical CCD camera system attached to the 2.1-m Otto-Struve Telescope (OST) at McDonald Observatory, USA. The new auto-guiding system diers from the original one in the following: instead of the cassegrain focus of the OST, it is attached to the nder scope; it has its own lter system for observation of bright targets; and it is controlled with the CQUEAN Auto-guiding Package, a newly developed auto-guiding program. Finder scope commands a very wide eld of view at the expense of poorer light gathering power than that of the OST. Based on the star count data and the limiting magnitude of the system, we estimate there are more than 5.9 observable stars with a single FOV using the new auto-guiding CCD camera. An adapter is made to attach the system to the nder scope. The new auto-guiding system successfully guided the OST to obtain science data with CQUEAN during the test run in 2014 February. The FWHM and ellipticity distributions of stellar proles on CQUEAN, images guided with the new auto-guiding system, indicate similar guiding capabilities with the original auto-guiding system but with slightly poorer guiding performance at longer exposures, as indicated by the position angle distribution. We conclude that the new auto-guiding system has overall similar guiding performance to the original system. The new auto-guiding system will be used for the second generation CQUEAN, but it can be used for other cassegrain instruments of the OST.