Co-injection molding is commonly used in daily accessories, car parts, and structural-reinforcement product. However, there are too many combinations of designs, materials, core/skin ration, and process condition, how to have suitable control of co-injection is very challenge. Furthermore, co-injection with multi-cavity system which is commonly applied in some forks structure products. However, due to the complicated nature, the inside mechanism for the combination of co-injection and multi-cavity is still not fully understood yet. In this study, we have proposed three kinds of multi-cavity systems to investigate cavity design influence on the core material penetration behavior. In Model 1 with three separated cavity system, the core penetration into individual cavity is strongly dependent on the timing of complete filled of the first cavity. Although flow rate conditions will affect the penetration history during the processing, it doesn’t change the final core penetration shape too much. On the other hand, we have also considered different thickness of connection between cavities in Model 2 (with 3.5 mm thick connector) and Model 3 (with 1.75 mm thick connector). During the early filling age (less than 90% of total volume filled), in Model 3, it is Branch 2 dominant; while in Model 2 it has no preference for Branch 1 and 2. The flow rate conditions have no significant effects for core penetration in this period. However, as more melt keeps flowing into cavities till the end of filling, the core penetration behavior is dramatically different at low flow rate (10 cm3/s). These results show that in the presence of different thickness of connector, the core penetration history and final shapes are significant different to that of separated cavity system (Model 1). Obviously, cavity design can alter the preference of core penetration from one side to the other. The results can help people for the management of skin/core distribution in co-injection molding.