The objective of this study is to develop and test a coarse-grained molecular dynamics framework to model microscale multiphase systems with different inter-particle interactions and recover emerging thermodynamic and mechanical properties at the microscale. A water-vapor model and a fused silica model are developed to demonstrate the capability of our framework. The former can reproduce the water density and surface tension over a wide range of temperatures; the latter can reproduce experimental density, tensile strength, and Young's modulus of fused silica. Therefore, the deformable solid model is implemented in the proposed framework. Validations of spatial scaling methods for solid, liquid, and multiphase systems suggest that the proposed framework can be calibrated at an arbitrary microscale and used at a different length scale without recalibration. Different values of wettability for a solid-liquid-vapor system that is characterized by the contact angle can be achieved by changing the solid-liquid inter-particle potential. Thanks to these features, the proposed coarse-grained molecular dynamics framework can potentially find applications in modeling systems in which multiple phases coexist and have substantial interactions.