Sound source localization (SSL) technology is a popular method for identifying the locations of noise sources, which serves as a prerequisite for noise control. Deep learning, as a data-driven tool, shows broad perspectives in the field of SSL with its powerful nonlinear fitting ability. The existing deep learning-based SSL methods only provide a two-dimensional (2D) representation of the sound source location and cannot obtain the specific coordinates of the sound source in three-dimensional (3D) space. Although traditional beamforming methods can be directly generalized to 3D scenes in principle, they suffer from the limitations of insufficient vertical resolution and high computational cost. Therefore, a 3D grid-free SSL method (3DGF) informed by deep learning is suggested in this study to enhance the accuracy and computational efficiency of 3D localization. First, the number of data channels is compressed to respect limited memory resources during the training process. Subsequently, a dense convolutional neural network (DenseNet) model is utilized to obtain the 3D spatial coordinates of the sound source using the processed 3D beamforming map as input. Since the coordinates are continuous and are not constrained by the grid of the beamforming map, the grid-free strategy presents more accurate localization results. Then, the effects of the volume of training data and the compression ratio are analyzed, respectively, in simulation, and the localization performance with different signal-to-noise ratios (SNRs) is also tested. Finally, by comparing 3DGF with DAMAS, both simulation and experimental results demonstrate that 3DGF improves the accuracy and efficacy of 3D localization. Meanwhile, its satisfactory generalization ability and robustness against noise highlight its potential for practical applications.