Co-injection molding, one of the multi-component molding methods, is commonly used in our daily life product. However, there are too many combinations of designs and parameters, how to properly control of co-injection is very challenge. Furthermore, co-injection with multi-cavity system is still not fully understood yet. In this study, we have focused on a nonsymmetrical multi-cavity system. First, we tried to find out how the viscosity difference effects on the variation of the interface between skin and core layers in co-injection molding. In A/A system, with a unique skin-to-core ratio and a fixed flow rate, general operation parameters have no significant effect on the change of the interface between skin and core. In A/B system, it generates longer and narrower locus than that of A/A system. On the other hand, in B/A system, it generates shorter and wider locus than that of A/A system. Moreover, in the presence of flow rate variation, as flow rate increased, the penetration distance of interface between the skin and core is reduced for A/A system. This reduction phenomenon on the penetration distance of the interface is also observed in A/B and B/A systems. Finally, the experimental study is also performed to verify the numerical predictions on the viscosity difference effects. Specifically, in the presence of flow rate variation, the numerical prediction on the interface between the skin and core is in a good agreement with the experimental data in trend.