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The internal stress effect on the scratching behavior in titanium single crystal is investigated by molecular dynamics simulations. It is introduced by applying the compressive/tensile pre-strain in this work. The friction force in the model with compressive pre-strain is higher than that with tensile pre-strain, which is related to the atomistic spacing and the distribution of pile-up. The dislocation mechanism is systematically illustrated that three types of <a> dislocations of edge dislocation loop, prism edge dislocation and screw dislocation dominate the plastic deformation. The coupling of dislocation loop and screw dislocation in the model with tensile pre-strain causes much more defects to remain in the matrix. However, when the model is applied by small compressive pre-strain, the dislocations left in the matrix are obviously decreased, reducing the internal crystal damage. Overall, the compressive/tensile internal stress has a distinguishing effect on the scratching behavior, which can be used for altering the friction and wear property of titanium.