This paper presents the numerical short-open calibration (SOC) method in the full-wave finite-element method (FEM) algorithm for accurate de-embedding of equivalent circuit parameters of a variety of 3-D nonplanar periodic guided-wave and discontinuity structures. It holds its attractive features in high efficiency and good accuracy as demonstrated in the method of moments algorithm, and further allows itself to be capable of characterization of 3-D nonplanar structures. By setting the reference plane along each feeding line as the perfect electric and magnetic conductors, i.e., PEC and PMC, the entire error box involved in each feeding line and impressed source can be characterized by using these two calibration standards, namely, short-and open-ended circuits. Formulation of ABCD matrix of this error box is described under the introduction of an impressed voltage at each port. Then, ABCD matrix of the core circuit structure can be effectively de-embedded or extracted. Finally, a few numerical examples are given to demonstrate the efficiency and accuracy of our proposed full-wave 3-D FEM-SOC approach in numerical de-embedding of 3-D nonplaner structures.