For high-gain multi-winding output series boost converters, during no-load startup, voltage offsets often occur among the output windings due to non-uniformity in winding coupling and differences in branch loads. This issue is particularly significant in scenarios where frequent no-load start-stop operations are required. Severe accumulation of voltage offsets can even lead to device breakdown, thereby threatening the stable operation of the converter and the reliability of the overall system. To address this issue, this paper proposes a novel autonomous voltage balancing scheme for multi-winding output branches during no-load startup. The aim is to achieve stable total output voltage by optimizing the traditional topology and introducing new control methods, enabling independent voltage hysteresis control for multiple winding outputs. Additionally, the scheme specifically addresses the high common-mode voltage issues during implementation, using specific control logic and compensation circuits to achieve voltage balancing and suppress voltage offsets during no-load startup. Furthermore, this scheme can be extended to various applications requiring precise control of output voltage, such as trickle charging and step load scenarios. This paper provides detailed theoretical analysis and experimental verification of the scheme, and builds a three-winding output series boost forward converter with an input of 48 V and an output of 800 V to validate the feasibility and effectiveness of the proposed scheme.