Skirted foundations are widely used in offshore and subsea engineering. Previous studies have shown that soil undrained shear strength variability has a notable impact on probabilistic analyses of skirted foundation bearing capacity. This study proposes an efficient machine-learning method to predict the uniaxial bearing capacity factors of skirted foundations under pure horizontal and moment loads, without relying on traditional time-consuming random finite element methods. A two-dimensional convolutional neural network is adopted to capture the potential correlation between soil random fields and bearing capacity factors. The proposed CNN-based model exhibits satisfactory prediction performance with regard to coefficients of variation and scale of fluctuations in two directions. Specifically, coefficient of determination (R2) values exceed 0.97, while root mean square error (RMSE) values remain below 0.13 for the surrogate model. In addition, more than 96% of the predictions are associated with a relative error of 5% or less, providing evidence of the proposed 2D-CNN model’s satisfactory prediction performance.