Drawing on constructivism and competency-based theory, this paper proposes an online learning system design method based on a knowledge graph, which breaks the traditional knowledge structure and builds a multi-dimensional competence framework of knowledge and skills with the goal of improving competence. A learning system with a knowledge graph as the underlying logic and linked digital learning resources was built. Teaching practice and empirical research were then carried out. First, the learning system was verified with a questionnaire. Second, taking the ability to “read English academic papers” as the learning task, experimental and control groups were created to evaluate the understanding of knowledge and skills, memory level, and comprehensive application ability of the participants. The results showed that the effectiveness and usability of the learning system were higher in the experimental group than in the control group in terms of total, knowledge, skill, and ability scores. Among these, total and ability scores showed significant differences, indicating that the system played a role in promoting the effect of online learning.