IC chips have gradually become smaller and smaller, and thus requires high packaging density. In chip packaging, accurate alignment of electronic components with respect to PCB is crucial for high quality packaging, especially in flip-chip assembly. In this paper, vision system is used to provide relative pose information between flip-chip and substrate. Based on this information, these two parts are aligned accurately using visual servoing. In order to achieve high accuracy alignment, a dual imaging system (DIS) is introduced in this work, which is composed of zoom lenses, beam-splitter, mirror, CCD, and LED illumination. It can simultaneously observe the solder bumps on flip-chip and the pattern of pads on substrate using one camera. Once the image frame containing flip-chip and substrate is obtained, their features are extracted from the preprocessed image. We can define the coordinate system of the solder bumps and the pattern using the extracted features. These coordinate systems enable us to obtain the position and orientation errors between the chip and the substrate. On the base of the measured errors, visual servoing method can determine the instantaneous velocity input of flip-chip at each servoing time and control the relative position and orientation precisely in an on-line manner. In addition to, we use SSD measure and particle filter for feature tracking for the uncertainty of dynamic model and fast tracking. We carry out a series of experiments for various conditions in order to evaluate the performance of the dual imaging system and the visual servoing algorithm as well.