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Abstract Room temperature semiconductor radiation detectors (RTSD) for X-ray and $$\gamma$$ γ -ray detection are vital tools for medical imaging, astrophysics and other applications. CdZnTe (CZT) has been the main RTSD for more than three decades with desired detection properties. In a typical pixelated configuration, CZT have electrodes on opposite ends. For advanced event reconstruction algorithms at sub-pixel level, detailed characterization of the RTSD is required in three dimensional (3D) space. However, 3D characterization of the material defects and charge transport properties in the sub-pixel regime is a labor intensive process with skilled manpower and novel experimental setups. Presently, state-of-art characterization is done over the bulk of the RTSD considering homogenous properties. In this paper, we propose a novel physics based machine learning (PBML) model to characterize the RTSD over a discretized sub-pixelated 3D volume which is assumed. Our novel approach is the first to characterize a full 3D charge transport model of the RTSD. In this work, we first discretize the RTSD between a pixelated electrodes spatially into 3 dimensions—x, y, and z. The resulting discretizations are termed as voxels in 3D space. In each voxel, the different physics based charge transport properties such as drift, trapping, detrapping and recombination of charges are modeled as trainable model weights. The drift of the charges considers second order non-linear motion which is observed in practice with the RTSDs. Based on the electron–hole pair injections as input to the PBML model, and signals at the electrodes, free and trapped charges (electrons and holes) as outputs of the model, the PBML model determines the trainable weights by backpropagating the loss function. The trained weights of the model represents one-to-one relation to that of the actual physical charge transport properties in a voxelized detector.