Retrograde intrarenal surgery (RIRS) is a widely utilized diagnostic and therapeutic tool for multiple upper urinary tract pathologies. The image-guided navigation system can assist the surgeon to perform precise surgery by providing the relative position between the lesion and the instrument after the intraoperative image is registered with the preoperative model. However, due to the structural complexity and diversity of multi-branched organs such as kidneys, bronchi, etc., the consistency of the intensity distribution of virtual and real images will be challenged, which makes the classical pure intensity registration method prone to bias and random results in a wide search domain. In this paper, we propose a structural feature similarity-based method combined with a semantic style transfer network, which significantly improves the registration accuracy when the initial state deviation is obvious. Furthermore, multi-view constraints are introduced to compensate for the collapse of spatial depth information and improve the robustness of the algorithm. Experimental studies were conducted on two models generated from patient data to evaluate the performance of the method and competing algorithms. The proposed method obtains mean target error (mTRE) of 0.971 ± 0.585 mm and 1.266 ± 0.416 mm respectively, with better accuracy and robustness overall. Experimental results demonstrate that the proposed method has the potential to be applied to RIRS and extended to other organs with similar structures.