Multifactor uncertain differential equations are powerful tools for studying dynamic systems under multi-source noise. A key challenge in this study is how to accurately estimate unknown parameters based on the framework of uncertainty theory in multi-source noise environments. To address this core problem, this paper innovatively proposes a least-squares estimation method. The essence of this method lies in constructing statistical invariants with a symmetric uncertainty distribution based on observational data and determining specific parameters by minimizing the distance between the population distribution and the empirical distribution of the statistical invariant. Additionally, two numerical examples are provided to help readers better understand the practical operation and effectiveness of this method. In addition, we also provide a case study of JD.com’s stock prices to illustrate the advantages of the method proposed in this paper, which not only provides a new idea and method for addressing the problem of dynamic system parameter estimation but also provides a new perspective and tool for research and application in related fields.