High catalytic efficiency is the continuous pursuit for the preparation of high-performance nanozymes. In this work, a Fe-Ce double variable-valence metals nanozyme (Fe-Ce-MOL) was constructed based on metal–organic layers (MOLs), a class of two-dimensional metal–organic frameworks with ultra-thin structure, for peroxidase (POD) mimicking. Fe-Ce-MOL exhibited significantly enhanced catalytic activity in comparison with that of natural horseradish peroxidase and single variable-valence metal nanozyme (Fe-Zr-MOL). Density functional theory calculations demonstrated that the Fe site of Fe-Ce-MOL had a stronger adsorption effect on H2O2 compared to Fe-Zr-MOL and more heat was released in the catalytic reaction of H2O2, making the reaction easier to occur. Moreover, there was more electron transfer between Fe and Ce double variable-valence metals, also accelerating the catalytic process. These results indicated that the ultra-thin structure of Fe-Ce-MOL provided more catalytic sites and Fe and Ce double variable-valence metals could regulate the process of oxidation–reduction and promote the efficiency of electron transfer synergistically. As a proof of concept, the proposed Fe-Ce-MOL was used in biosensing and antibacterial applications. These results suggested that Fe-Ce-MOL had great potential as a new-generation nanozyme. This work pioneers a new approach for the rational design of highly efficient nanozymes.