This paper aims to explore a new-type Mo-based composite conversion coating on 6061 aluminum alloy, systematically evaluate its corrosion resistance, and further reveal the formation mechanism. The effects of pH, conversion time (CTI) and H2ZrF6 content on the corrosion resistance were determined by the dropping test and electrochemical tests, and the average corrosion rate (ACR) in neutral 3.5 wt.% NaCl solution under different temperatures was calculated by the immersion test. The micro-morphology and phase compositions were systematically investigated by SEM, EDS and XPS. The results showed that the optimal pH and CTI were 4.5 and 12 min respectively, and the most suitable addition amount of H2ZrF6 was 1.2 mL/L. The micro-morphology of the Mo/Ti/Zr conversion coating (MoTiZrCC) under the best conversion condition was relatively smooth and dense, and its phase compositions mainly consisted of MoO3, Mo2O5, TiO2, ZrO2 and Al2O3. The MoTiZrCC could significantly improve corrosion resistance with the lower icorr and higher Rp, and the ACR of the MoTiZrCC could be reduced to 16.7% of the Al alloy matrix. Additionally, based on the above results, the formation mechanism for the MoTiZrCC was logically deduced.