Effect of nanopore-water/nanopore-protein interaction on electrophoresis mobility of protein translocation is studied with coarse-grained molecular dynamics simulation. With steer molecular dynamics, friction coefficient and friction of protein under different interactions are analyzed. It shows that protein adhesion to nanopore wall has weak effect on protein translocation through a nanopore, while nanopore-water interaction has significant effect on electrophoretic mobility and friction coefficient. The increase of interaction between nanopore and water increases difference between movement of water molecules near nanopore wall and protein, which leads to increase of friction coefficient of protein translocation. As a result, mobility electrophoresis of protein through nanopore is affected. It provides a theoretical guidance for the design of nanopore materials.