In roll-to-roll digital maskless lithography (R2R DML) equipment, it is difficult to achieve high quality, owing to surface deformation that affects the pattern position. To address this issue, we simulated the patterning results of R2R DML to analyze the relationship between positional errors and pattern quality. Errors perpendicular to the pattern direction exhibited a 1.3–2 times greater effect on the linewidth and line edge roughness compared to those parallel to this direction. We confirmed that positioning errors could lead to defects in which the photoresists were not fully exposed. Finally, through simulations, we found that the effect of positional errors could be reduced by controlling the array spot separation length.