Sclerotinia stem rot is a widespread soybean disease commonly found worldwide. In Northeast China, the incidence rate of soybean Sclerotinia stem rot exceeds 60%, severely affecting soybean yield and economic benefits. Therefore, it is imperative to investigate the pathogenetic mechanisms of Sclerotinia sclerotiorum, the fungus that causes Sclerotinia stem rot, and to develop effective detection and identification methods. This article introduces the molecular-level pathogenic mechanisms of S. sclerotiorum and provides a comprehensive review of the existing detection methods for the fungus, including traditional, serological, and molecular biological detection methods. With a detailed account of the sensitivity, specificity, and applicability of existing detection methods, this review compares and evaluates the advantages and limitations of various methods and preliminarily explores the detection model for S. sclerotiorum. The aim of this study was to provide a reference for the identification and detection of Sclerotinia stem rot in soybeans, offering technical support for early disease detection and a theoretical basis for sustainable development of the soybean industry.