In the third millennium, people deal with multiple, diverse, and complicated problems as they cannot possess full control over the information, which is constantly produced and accumulated. Having a high skill of critical thinking for assessing the results of different issues and decision making about them based on evidences is an unavoidable necessity. The researchers of this work proposed a model with seven factors (components) for critical thinking in e-learning environments. The statistical group of this work is the M.Sc. medical education students of  AZAD university e-learning environments, and the students of the same field from Islamic Azad University traditional education system studying during 2011-2012. Among the research community, 47 members were selected based on a simple random method and divided into two trial (with 23 members) and reference (with 42 members) groups. To train the trial group, the seven-factor critical thinking training scale was utilized in e-learning environments in 15 sessions with empirical sciences course. In the reference group, the same seven-factor critical thinking training scale was used in the classroom environment in lecturing in 15 sessions with empirical sciences course. The model factors and components are challenge, representation, creation of opportunity, creation of motivation, logical analysis, encouragement, responsibility, and commitment. Both groups were subject to two pretest and posttest steps within two trial groups, which were considered as reference to each other. Both groups responded to the Watson- Glaser™ Critical Thinking Appraisal within two pretest and posttest steps, while the covariance analysis statistical test was used for analysis of the results. The results indicate significant difference between the scores between trial and reference groups in improving the critical thinking of the students in terms of inferential, assumption detection, deduction, interpretation, and logical reasoning evaluation components (p=0.001). According to the results, in terms of improving critical thinking, the trial group trained in the e-learning environment indicates higher scores as compared to the group trained in the traditional classroom environment.