This study was designed to investigate effects of a Direct Instruction program on learning skills and learning motivation. Direct Instruction(DI) is known as one of the most effective instructional method for learning disabilities but its influence on learning skills and motivation is still in debate. The participants of this project was 26 middle school students who were found to have learning difficulties. Sixteen of the participants received DI at least for one semester (10 sessions) during two years of the DI project||| and the other ten students were participated as a comparison group. Survey about learning skills and learning motivation was conducted before and at the end of the two-year DI project. The result of repeated measure mixed within-between ANOVA showed that there was a significant difference between DI group and comparison group on learning skills||| especially on self-regulation||| class-listening||| and reading skills. There was no significant difference found regarding learning motivation. There was a positive correlation between the growth in learning skills and the academic achievement. This relationship suggested the effect of DI on learning skills would help students to succeed in academic achievement.