In this paper, a de-embedding method to extract the performance of a Through-Silicon-Via (TSV) pair is proposed, using a set of specially designed test patterns to remove the pads and connection trace. Considering in real implementations, wafer probe measurements are required to access the test structures, and any errors in the probe calibration affect the test pattern measurements, a micro-probe model is built in with the test. Short-Open-Load (SOL) calibration method is used with the simulation results to calibrate or correct to the tips of the micro-probe used in all test patterns. Calibrated responses for the test patterns consisting of probing pads, traces and TSV pair, thus are used with previously proposed de-embedding algorithm to characterize the TSV pair. The effectiveness and the robustness of the de-embedding method against probe calibration errors are tested with the full wave simulation results and analytical calculations.