The aim of this research was to review past empirical studies about systems thinking in science education in order to understand the applied grade levels and subject areas, the analytical framework for systems thinking, and its trends in teaching and assessment. We searched for research articles published from 2000 to 2019 in the SCOPUS and Web of Science database and found 20 qualified studies. The results showed that most studies were conducted at junior high schools and senior high schools. Some studies were conducted at the elementary school level and found gains in fundamental competence of systems thinking. The most frequently applied subject areas were ecology, biology, and earth science. In this review, no studies applied systems thinking in physics. This indicates that systems thinking might not be suitable for all subject areas of science. In terms of the analytical framework for systems thinking, different studies invented different frameworks. The common features of the systems thinking framework include components recognition, as well as the mutual interactions and influence of different components. Regarding assessment for systems thinking, some studies used multiple assessments, and the most commonly used types of assessments were open-ended questions and interviews. Many studies adopted a variety of teaching activities and included knowledge integration activities. Some studies also used computer simulations to support learning. For future research, we suggest investigating the learning progression of systems thinking or conducting longitudinal studies by applying the available analytical framework of systems thinking. Future studies can also apply computer technology in the assessment of systems thinking. Finally, we offer some specific suggestions for teaching and assessments of systems thinking.