Aeromagnetic measurement plays an important role in mineral exploration, but unmanned aerial vehicles generate maneuvering noise during aerial flight, which negatively impacts the accuracy of aeromagnetic measurement data. Therefore, aeromagnetic compensation is an indispensable step in aeromagnetic data processing. The multicollinearity of variables in the aeromagnetic compensation model based on linear regression affects its accuracy, resulting in a large difference in the compensation effect of the same group of compensation coefficients in different directions. In order to obtain high-quality aeromagnetic data, this study proposes an adaptive model-based method for suppressing aeromagnetic maneuvering noise. First, due to the fact that the variables that cause multiple collinearity in the compensation model are related to the flight heading, the model variables are adaptively assigned to each heading based on the characteristics of the variable data for different headings. The compensation model is optimized and improved, and the impact of multiple collinearity is thus suppressed. In adaptive modeling, variables with greater significance and smaller multicollinearity are automatically allocated to build the optimal heading model, and then high-precision compensation coefficients are obtained. This algorithm was applied to the data collected by a certain unmanned aerial vehicle aeromagnetic measurement platform in Ma’anshan and compared with traditional methods. The experimental results show that the adaptive modeling-based aeromagnetic compensation algorithm is superior to traditional algorithms, with fewer errors and a higher improvement ratio. Hence, the method can effectively solve the ill-conditioned problem of a model affected by multicollinearity and further improve its compensation accuracy and robustness. Moreover, the feasibility and value of this algorithm were verified in actual mineral resource detection.