In hydropower dominated power systems, low-frequency oscillations (LFO), that challenge the safe and stable operation of the system, occur from time to time. Although the study of system damping is an important way to reveal the mechanism of LFO, relevant analysis is mainly based on simplified models that consider a single scale, leading to an incomplete understanding of the phenomenon. Against this background, a cluster of hydropower units in a real power station is taken in this paper as the research object. Firstly, a refined non-linear model of the hydroturbine regulation system with the layout of three units sharing one common tailrace tunnel is established and validated based on mechanism analysis and measured data. Then, an accurate quantitative evaluation method of damping for complex systems is proposed to overcome the application limitations of traditional methods. Finally, the variation laws of the damping of a hydropower unit with the hydraulic-electrical network structures and the operating conditions, studied from the scales of hydraulic coupling and electrical coupling, respectively, reveal the influence mechanism of the hydraulic-mechanical-electrical coupling on unit damping. The results show that the increase in the complexity of the hydraulic or electrical network structure will reduce the damping of the hydropower unit, which changes from 1.3860 to -1.3223 for hydraulic factor and from 1.1869 to -0.8817 for electrical factor. The operating conditions of the adjacent units have different degrees of influence on the damping of the unit itself due to their hydraulic or electrical connections. Some measures to suppress LFO are also given.