High-speed and precision positioning are fundamental requirements for high-acceleration low-load mechanisms in integrated circuit (IC) packaging equipment. In this paper, we derive the transient nonlinear dynamicresponse equations of high-acceleration mechanisms, which reveal that stiffness, frequency, damping, and driving frequency are the primary factors. Therefore, we propose a new structural optimization and velocity-planning method for the precision positioning of a high-acceleration mechanism based on optimal spatial and temporal distribution of inertial energy. For structural optimization, we first reviewed the commonly flexible multibody dynamic optimization using equivalent static loads method (ESLM), and then we selected the modified ESLM for optimal spatial distribution of inertial energy; hence, not only the stiffness but also the inertia and frequency of the real modal shapes are considered. For velocity planning, we developed a new velocity-planning method based on nonlinear dynamic-response optimization with varying motion conditions. Our method was verified on a high-acceleration die bonder. The amplitude of residual vibration could be decreased by more than 20% via structural optimization and the positioning time could be reduced by more than 40% via asymmetric variable velocity planning. This method provides an effective theoretical support for the precision positioning of high-acceleration low-load mechanisms.