This longitudinal study explored the effects of a Cooperation-driven Socioscientific Issue (CDSSI) intervention on junior high school students' perceptions of critical thinking (CT) and self-regulation (SR) in Taiwan. Forty-nine grade 7 students were randomly selected as an experimental group (EG) to attend a 3-semester 72-hour intervention; while another 49 grade 7 students from the same school were randomly selected as the comparison group (CG). All participants completed a 4-wave student questionnaire to assess their perceptions of CT and SR. In addition, 8 target students from the EG with the lowest scores on either CT or SR were purposefully recruited for weekly observation. These target students and their teachers were interviewed one month after the intervention in each semester. Analyses of covariance and paired-wise t-tests revealed that the EG students' perceptions of CT and SR in learning science were improved during the study and were significantly better than their counterparts' at the end of the study. Systematic interview and classroom observation results were consistent with the quantitative findings. This study adds empirical evidence and provides insights into how CDSSI can be integrated into planning and implementing effective pedagogical strategies aimed at increasing students' perceptions of CT and SR in learning science.