This paper presents an evaluation study of an innovative and theory-based initial teacher education course entitled Learning Study, the aim of which is to develop the instructional design and teaching competency of pre-service teachers in Hong Kong. The Learning Study course is offered to all second year students as part of the Bachelor of Education programme of the biggest teacher education institute in Hong Kong. The course comprises a series of theory-based tutorials, supportive consultation meetings, and a research lesson practicum. To assess the effectiveness of the course, a framework of representation, decomposition, and approximation of practices was adopted to describe and analyse the teaching of practice. A total of 341 pre-service teachers participated in a quasi-experimental design questionnaire survey. A structural equation model was applied to explore the relationship between the activities of their learning process and their learning outcomes. Theory-based tutorials, consultative support, and research practicums are confirmed to be the predictors of learning outcomes which include instructional design skills, teaching competency, and clinical experience. This paper proposes Learning Study as a model to help pre-service teachers develop their instructional design skills and teaching competency.