The structure and assembly process of Chip Shooter (CS) machine are studied. The factors of engineering practice such as the component size and machine structure etc. are considered. The assembly optimization model of Printed Circuit Board (PCB) on CS machine is formulated. A hybrid genetic algorithm (HGA) which combine with Polychromatic Sets (PS) and Genetic Algorithm (GA) is presented. A binary piece-wise coding method is proposed. In the individual chromosome, feeder arrangement and component placement sequence is described simultaneously. Constraint model is used to consider the impact of component size on the assembly speed and the feeder arrangement of CS machine. Meanwhile the constraint model improved the quality of initial population, ensured the effectiveness of GA operation and narrowed the search space of GA obviously. Calculation example indicated that HGA optimize the component sequence and feeder arrangement simultaneously and achieve excellent practicability. The assembly efficiency of CS machine is improved obviously.