Critical thinking (CT) includes cognitive skills such as inference, analysis, interpretation, evaluation, explanation, and self-regulation. Previous studies did not pay much attention to CT cognitive skills although they underlie the successful writing in an academic setting. Thus, the present study aimed to investigate the impact of CT cognitive skills on the academic writing of second language learners of Japanese (JSL). Fifty-four JSL learners were randomly divided into three groups: the critical thinking group (CT), the academic writing group (AW), and the control group (CG). Participants in the CT group received an essay writing instruction focused on CT cognitive skills. The participants in the AW group received conventional essay writing instructions. The participants in CG received no instruction. All participants wrote an argumentative essay. Using an analytical academic writing rubric, two raters evaluated the essays in terms of overall quality and the specific components of content, organization, and coherence. The results show that the participants in the CT group had significantly higher scores for overall quality as well as each of the specific components compared with the other two groups. This finding suggests that CT cognitive skills play a critical role in enhancing text quality.