Miniscrews are widely used in orthodontics as an anchorage device while aligning teeth. Shear stress in the miniscrew-bone interface is an important factor when the miniscrew makes contact with the bone. The objective of this study was to analyze the shear stress and force in the screw-bone interface for varying Cortical Bone Thickness (CBT) using Finite Element Analysis (FEA). Varying CBT of 1.09 mm (1.09CBT) and 2.66 mm (2.66CBT) with miniscrews of Ø1.2 mm, 10 mm length (T1), Ø1.2 mm, 6 mm length (T2) and Ø1.6 mm, 8 mm length (T3) were analyzed. Six Finite Element (FE) models were developed with cortical, cancellous bone, miniscrews and gingiva as a prism. A deflection of 0.1 mm was applied on the neck of the miniscrews at 0°, +30° and −30° angles. The shear stress and force in the screw-bone interface were assessed. The results showed that the CBT affects the shear stress and force in the screw-bone interface region in addition to the screw dimensions and deflection angulations. T1 screw generated lesser shear stress in 1.09CBT and 2.66CBT compared to T2 and T3 screws. Higher CBT is preferred for better primary stability in shear aspect. Clinically applied forces of 200 gms to 300 gms to an anchorage device induces shear stress in the miniscrew-bone interface region might cause stress shielding. Thus, clinicians need to consider the effect of varying CBT and the size of the miniscrews for the stability, reduced stress shielding and better anchorage during orthodontic treatment.