Cone Penetration Test (CPT) is widely utilized to gain regular geotechnical parameters such as compression modulus, cohesion coefficient and internal friction angle by transformation model in the site investigation. However, it is challenging to obtain simultaneously the unknown coefficients and error of a transformation model, given the intrinsic uncertainty (i.e., spatial variability) of geomaterial and the epistemic uncertainty of geotechnical investigation. A Bayesian approach is therefore proposed calibrating the transformation model based on spatial random field theory. The approach consists of three key elements: (1) three-dimensional anisotropic spatial random field theory; (2) classifications of measurement and error, and the uncertainty propagation diagram of geotechnical investigation; and (3) the unknown coefficients and error calibration of the transformation model given Bayesian inverse modeling method. The massive penetration resistance data from CPT, which is denoted as a spatial random field variable to account for the spatial variability of soil, are classified as type A data. Meanwhile, a few laboratory test data such as the compression modulus are defined as type B data. Based on the above two types of data, the unknown coefficients and error of the transformation model are inversely calibrated with consideration of intrinsic uncertainty of geomaterial, epistemic uncertainties such as measurement errors, prior knowledge uncertainty of transformation model itself, and computing uncertainties of statistical parameters as well as Bayesian method. Baseline studying indicates the proposed approach is applicable to calibrate the transformation model between CPT data and regular geotechnical parameter within spatial random field theory. Next, the calibrated transformation model was compared with classical linear regression in cross-validation, and then it was implemented at three-dimensional site characterization of the background project.