We conducted laboratory experiments to investigate the influence of surface wettability on Dense Nonaqueous Phase Liquid (DNAPL) migration in a rough-walled fracture at various groundwater flow conditions. A glass replica of a granite sample containing a rough-walled single fracture was made, and DNAPL migration experiments were carried out with the replica whose surface wettability was controlled by using several NAPL exposures. In the experiments, we observed different migration paths of DNAPL among the hydrophilic, weakly hydrophobic, and strongly hydrophobic surfaces in the linear flow regime, whereas there was little difference in the nonlinear flow regime. The modified invasion percolation model was used to analyze the quantitative influence of the wettability change and groundwater flow on DNAPL migration paths in a rough-walled fracture, and suggested that the wettability is important to determine the DNAPL migration path in the linear flow regime but inertial force of groundwater becomes strong enough to overcome the influence of the wettability in the nonlinear flow regime.