The acquisition of critical thinking (CT) as one of the 21st century skills is categorically crucial. Therefore, the effective training of CT skills in terms of learning activities needs detailed exploration. This study applied the ethno-inquiry model in an e-learning platform and evaluated its impact on the CT skills of preservice science teachers (PSTs). The experimental design employed the randomized pretest-posttest control design involving 62 PSTs as participants, divided equally into an experimental and control group. Participants’ CT skills were assessed using essay tests. The tests focused on the CT skills dealing with analysis, inferencing, evaluation, and decision-making indicators. The CT scores were analyzed using parameters of the average pretest-posttest. The learning implementation effects were calculated using a paired t test and analysis of covariance (ANCOVA) at the significance level of .05. The findings demonstrated that the CT scores for the experimental group increased from the less critical to the critical level. This result was better than that of the control group. Similarly, the improvement of individual CT performance was better in the experimental group. Based on the results of the analysis, the t test and ANCOVA of both groups confirmed that the ethno-inquiry model had a significant effect on the CT skills of participants. The results thus provide convincing evidence of the essential roles of the ethno-inquiry model in science learning and it is therefore recommended that the model be implemented in science classes.