The large-scale variable renewable energy (VRE) forces hydropower to smooth out more frequent and violent load/supply fluctuations in cascade hydropower-VRE hybrid systems (CHVHS), threatening the hydropower units safety. This paper proposes a short-term optimization operation model, considering the vibration in both the stable operation and regulation process, which minimizes the whole-process vibration for a CHVHS. Particularly, the traversing depth (TD) is defined for the first time and combined with the traversing time to quantify the cost of traversing vibration zone (VZ), and a complete vibration avoidance strategy applicable to multiple VZs of multiple units is proposed. Finally, the cascade hydropower stations in Hongshui River Basin are selected as a case study. The validity and superiority of the model are verified by comparing with two conventional operation models from the hydropower station and unit perspectives under different load curves, hydrology, wind speed and solar intensity scenarios. The proposed model enables the hydropower unit not to operate in the VZ, and its TD is reduced by 54.28 % and 55.28 % compared to the two conventional models respectively. The approach provides a safe and stable operation pattern that considers whole-process vibration for a CHVHS, mitigating exacerbated vibration from hydropower units compensating for VRE uncertainty.