2.5D IC is an important transition product of 3D IC in the next generation. It has very important commercial value. However, at present 2.5D IC package process has numerous issues that need to be overcome, especially for interface delamination caused by warpage under reflow temperature. Conventionally, the material adopted for the passivation (PA) layer in 2.5D IC package is inorganic metal glass. But for being cost-effective, organic polymer is another choice. Accordingly, the adhesion strength between organic PA and underfill (UF) layers is a critical issue. In this paper, molecular dynamics (MD) simulation is applied to analyze the interface adhesion between organic PA and UF layers affected by five chemical PA types, compensating for essential limitations of experimental and FE simulation analysis. From the pull test curves of MD simulation, the adhesion strength of different PA types to UF layers corresponding to molecular interaction mechanisms such as chemical bond force, non-bond force including Coulomb electrostatic force and van der Waals adsorption, and mechanical interlocking force are examined. The present results reveal that the adhesion strength of the five PA types to UF layers display significant variations, which could be attributed to different strength characteristics in molecular interaction mechanisms due to different PA chemical structures. The ranking order for the maximum adhesion strengths of the pull test curves with five PA chemical types is of acrylic, BCB, epoxy resin of novolak, polyimide, and PBO, types, respectively. The maximum adhesion strengths of the pull test curves with five chemical PA types exhibit the obviously discrepancies, which demonstrates that different PA chemical types play the key role to affect the adhesion strength of PA and UF layers. With regard to the maximum adhesion strength of PA and UF layer affected by the molecular interaction mechanisms, the key influence factors should be Coulomb electrostatic force, van der Waals adsorption, and the mechanical interlocking force because the trend variations are highly related with the value distributions of the maximum adhesion strengths, but due to the page restrictions, the analysis results and interpretations are not presented here. Based on the present study, it could be further extended to establish the design rule for the material development and synthesis of the workability performance promotion of organic PA or UF.