This study aimed to evaluate the effects of intervention using graphic organizers on the cognitive and affective improvement of students with intellectual disability (ID), with learning disability (LD), without disability, and at-risk learners in Korea. A total of 49 peer-reviewed journals and dissertations for the last 20 years were included for conducting this meta-analysis. The overall effect size of intervention using a graphic organizer was 0.78 (d) (95% CI [0.63, 0.94], [tau superscript 2]= 0.28) using a random-effects model. In order of strongest to weakest effects, at-risk learners (d = 1.38), students with LD (d = 1.15), students with ID (d = 0.76), and students without disability (d = 0.52). Among student variables, there is no statistically significant difference by school level, but by school type. Among intervention variables, instruction in math (d = 1.43) and Korean (d = 0.96); cognitive mapping (d = 1.05); 1-19 times, 1-9 weeks, 3-5 times per week; and small-size groups were the most effective intervention conditions. While several variables showed significant subgroup differences, meta-regression analyses revealed that only group size and frequency were significant moderators after controlling for other factors. In summary, intervention using a graphic organizer was more effective for students with disability and at-risk students than it was for students without disability.