In thread milling, there exists a trade-off between thread manufacturing efficiency and thread quality. In this study, an integrated design of spindle speed modulation (SSM) and cutting vibration suppression (CVS) controls using a disturbance observer were developed to simultaneously ensure superior quality and high manufacturing efficiency. The proposed integrated design not only controls the cutting torque while suppressing cutting vibrations but also ensures cost-effectiveness and mitigates the installation problems prevalent in existing sensor-based methods. The SSM control uses a disturbance observer to estimate the cutting torque required on the spindle during thread milling. The estimated cutting torque is used as a feedback signal so that the SSM control can modulate the spindle speed to make the cutting torque achieve a preset torque command. To further avoid cutting vibrations in thread milling, the CVS control analyzes the estimated cutting torque, detects the occurrence of cutting vibrations, and then adjusts the torque command of the SSM control to suppress the cutting vibrations. In this study, thread milling experiments were performed on a computer numerical control milling machine using the workpiece with stacked materials. The feasibility and performance of the proposed integrated design were validated by experiments.