Web-based scientific inquiry learning is characterized as providing an autonomy-supportive environment for students to solve scientific problems. However, as a complementary approach for improving students' learning, structure-supportive strategies in a web-based learning environment deserve further exploration. Whilst both teachers and platforms could make essential contributions in providing structure support, research findings concerning how teachers could successfully interact with the platform in such an environment are scarce. Grounded on self-determination theory, two quasi-experimental studies with pre and post measurements were conducted to address two questions. First, whether structure support could improve students' inquiry learning in an autonomous web-based inquiry learning environment? Second, what is the relationship between teachers and platforms in doing this? As hypothesized, study 1 provides empirical evidence on the effectiveness of applying structure-supportive instructional strategies in autonomous web-based scientific inquiry. Study 2 confirmed that students performed best in the class with high structure support provided by both teachers and platforms. The results shed light on the positive impacts of integrating both autonomy and structure support and emphasize the critical role of teachers in a web-based inquiry learning environment. Additionally, they infer a possible causal link between the efficient application of structure strategies and students' learning outcomes.