Programming is a skill that requires high levels of logical thinking and problem-solving abilities. According to the Curriculum Guidelines for the 12-Year Basic Education currently implemented in Taiwan, programming has been included in the mandatory courses of middle and high schools. Nevertheless, the guidelines simply recommend that elementary schools conduct fundamental instructions in related fields during alternative learning periods. This may result in the problem of a rough transition in programming learning for middle school freshmen. To alleviate this problem, this study proposes an augmented reality (AR) logic programming teaching system that combines AR technologies and game-based teaching material designs on the basis of the fundamental concepts for seventh-grade structured programming. This system can serve as an articulation curriculum for logic programming in primary education. Thus, students are able to develop basic programming logic concepts through AR technologies by performing simple command programming. This study conducted an experiment using the factor-based quasi-experimental research design and questionnaire survey method, with 42 fifth and sixth graders enrolled as the experimental subjects. The statistical analysis showed the following results: In terms of learning effectiveness, both AR-based and traditional learning groups displayed a significant performance. However, of the two groups, the former achieved more significant effectiveness in the posttest results. Regarding learning motivation, according to the evaluation results of the Attention, Relevance, Confidence, and Satisfaction (ARCS) motivation model, the AR-based learning group manifested significantly higher levels of learning motivation than the traditional learning group, with particularly significant differences observed in the dimension of Attention. Therefore, the experimental results validate that the proposed AR-based logic programming teaching system has significant positive effects on enhancing students' learning effectiveness and motivation.