Developmental dyscalculia (DD) is a specific mathematical learning disability, with a prevalence of around 3%-7% in the school-aged population. It negatively affects individuals, and even the national, development. Previous DD-intervention programs usually targeted on numerosity, number, simple arithmetic, or even general cognitive ability. The current study investigated the effect that a long-term (2-3 years) abacus course had on the prevalence of DD. Twelve classes of students were tested, half of which received an abacus course. Results showed that although no children were diagnosed as DD in the abacus classes, its prevalence was 6.4% in the control classes. Students with an abacus course demonstrated better performance in arithmetic computation and spatial short-term memory after controlling for age, gender, grade, and other basic cognitive abilities. The results suggest that the abacus course could be an effective tool for DD intervention in natural education settings.