Co-Injection Molding and multi-cavity molding are very common processes for plastic manufacturing. These two systems are sometimes combined and applied to some structure products. The core penetration and flow balance control problems are very difficult to manage. The inside mechanism of co-injection multi-cavity system is not fully figured out yet. In this study, we have focused on the penetration phenomena of core-material in a co-injection multi-cavity molding. The dynamic penetration behavior of core is very sensitive to injection speed and skin/core ratio. The longest core penetration has been shown to change dramatically from one runner to the other. In addition, the core penetration behavior will display imbalance at the end of filling. The more core ratio it is, the longer core penetration flows through runner to cavity. However, due to the multi-cavity geometrical structure, the balance of the core penetration for multi-cavity is still challenging. Finally, the simulation is validated with some literature. The results showed that both simulation and experiment are in a good agreement in trend.