In this study, CrSiN nano-composite ceramic films with optimized structure were prepared at low temperature using MIS-HiPIMS technique, owing to improved utilization of the high ionization characteristic of HiPIMS under specially designed synchronized pulsed-bias working mode. The correlations of the synchronized pulsed-bias width, the chemical composition, microstructure evolution, mechanical properties and tribological behaviors were studied systematically. According to the results, the waveforms of the pulsed bias experienced obvious fluctuating periods, indicating fluctuating intensities of positive ions arrived at the substrates. Meanwhile, the fluctuating duration increased with increasing synchronized pulse-width, providing an effective way of adjusting the energetic-ion flux for improved bombardment of the growing film. Therefore, obvious microstructure refinement of the as-deposited CrSiN films had been achieved. Due to optimized ion bombardment, the CrSiN films evolved from a coarse and transgranular columnar structure to a more densified columnar structure with the mixture phases of hcp-Cr2N, fcc-CrN as well as a-Si3N4. Moreover, the hardness and elastic modulus of the CrSiN films were also elevated significantly, to the maximum values of 20.2 GPa and 348.3 GPa, respectively. Furthermore, with the best mechanical properties as well as the highest density, the optimized CrSiN film deposited at 400 μs also displayed the most excellent wear resistance, with the wear rate as low as 9.1 × 10−16 m3/N.m. This study not only proposes a method of optimizing the structure and tribological properties of CrSiN nano-composite ceramic films at relatively low temperature, and also enriches the property database of CrSiN films which could expand their application in fields involving thermal-sensitivity materials.