In this paper, the NAPL contamination transportation concerning with the wettability in the single filled fracture was studied by the Shan-Chen multi-component multiphase lattice Boltzmann model. With the help of the model, the contact angle of the non-wetting phase and wetting phase interface at a solid wall is adjustable. By considering a set of appropriate boundary conditions, the fractured conductivity under the NAPL contamination blocks the channels in the single filled fracture was investigated. The conductivity Kf is dependent of the NAPL contamination content. The different Simulated results show that the lattice Boltzmann method is a very instrumental method for simulating and studying the immiscible multiphase flow problems in single filled fracture.