The objective of this paper is to define normal values of a novel 3D cephalometric analysis and to define the links through an artificial neural network (ANN). Methods: One hundred and fifteen CBCTs of Class I young patients, distributed among gender-adjusted developmental groups, were selected. Three operators identified 18 cephalometric landmarks from which 36 measurements were obtained. The repeatability was assessed through the ICC. Two-dimensional values were extracted by an automatic function, and the mean value and standard deviation were compared by paired Student’s t-tests. Correlation coefficient gave the relationships between 2D and 3D measurements for each group. The values were computed with the ANN to evaluate the parameters normality link and displayed by Pajek software. Results: The ICC assessed an excellent (≥0.9) repeatability. Normal values were extracted, and compared with 2D measurements, they showed a high correlation on the mid-sagittal plane, reaching 1.00, with the lowest 0.71 on the lateral plane. The ANN showed strong links between the values with the centrality of the go-sagittal plane compared to the rest. Conclusions: The study provides a set of 3D cephalometric values obtained by the upper and lower 95% CI for the mean divided into the developmental stage subgroups. The two-dimensional measurements showed variable concordance, while the ANN showed a centrality between the parameters.