Accurately measuring the moisture content (MC) of square timber is crucial for ensuring the quality and performance of wood products in wood processing. Traditional MC detection methods have certain limitations. Therefore, this study developed a one-dimensional convolutional neural network (1D-CNN) model based on the first 8 nanoseconds of ground-penetrating radar (GPR) signals to predict the MC of square timber. The study found that the mixed-species model exhibited effective predictive performance (R2 = 0.9864, RMSE = 0.0393) across the tree species red spruce, Dahurian larch, European white birch, and Manchurian ash (MC range 0%–133.1%), while single-species models showed even higher accuracy (R2 ≥ 0.9876, RMSE ≤ 0.0358). Additionally, the 1D-CNN model outperformed other algorithms in automatically capturing complex patterns in GPR full-waveform amplitude data. Moreover, the algorithms based on full-waveform amplitude data demonstrated significant advantages in detecting wood MC compared to those based on a traditional time–frequency feature parameter. These results indicate that the 1D-CNN model can be used to optimize the drying process and detect the MC of load-bearing timber in construction and bridge engineering. Future work will focus on expanding the dataset, further optimizing the algorithm, and validating the models in industrial applications to enhance their reliability and applicability.