Ultrasound imaging (USI) is the gold standard in the clinical diagnosis of thyroid diseases. Compared with two-dimensional (2D) USI, three-dimensional (3D) USI could provide more structural information. However, the unstable pressure generated by the hand-hold ultrasound probe scanning can cause tissue deformation, especially in soft tissues such as the thyroid. The deformation is manifested as tissue structure being compressed in 2D USI, which results in structural discontinuity in 3D USI. Furthermore, multiple scans apply pressure in different directions to the tissue, which will cause relative displacement between the 3D images obtained from multiple thyroid scans. In this work, we proposed a framework to minimize the influence of the variation of pressure in thyroid 3D USI. To correct pressure artifacts in a single scanning sequence, an adaptive method to smooth the position of the 2D ultrasound (US) image sequence is adopted before performing volumetric reconstruction. To build a whole 3D US image including both sides of the thyroid gland, an iterative closest point (ICP) based registration pipeline is adopted to eliminate the relative displacement caused by different pressure directions. Our proposed method was validated by in vivo experiments, including healthy volunteers and volunteers with thyroid nodules at different grading levels. The thyroid gland and nodule are rendered intelligently in the whole scanning region to facilitate the observation of 3D USI results by the doctor. This work might make a positive contribution to the clinical diagnosis of diseases of the thyroid or other soft tissues.