Childhood obesity and physical inactivity have been a growing health problem all over the world, leading to health consequences that extend into adolescence and adulthood, such as diabetes, stroke, or osteoarthritis. Motor skill competence and its predictive and protective relationships with body weight/adiposity and physical activity participation have been studied extensively in recent decades. However, motor proficiency determined by current standardized assessments of fundamental motor skills (e.g., running, jumping, kicking, striking) is necessary yet not sufficient for promoting a healthy weight status and physically active lifestyle in late childhood and adolescence. To alleviate this insufficient scalability, we proposed using advanced movement skills (AMS), a higher level of motor skills, defined as movement skills characterized by the elevated complexity/functionality with the emphasis on the interaction between two linked movements/skills (e.g., single-leg hopping for a maximum distance and with a stable landing). Since demonstrating adequate discriminating ability and significant predictive power of body adiposity, competence in AMS is suggested to represent the motor functioning required for developing and sustaining healthy practices. In addition, the construct validity and test-retest reliability of AMS tests with the innovative dual-outcome scoring system were verified through a combination approach of factor analysis and item response theory modeling. Proficiency in AMS tests, as a valid, reliable, and feasible assessment set, refines the dynamic relationship between motor competence and physical health in childhood and adolescence. Our results are significant by providing a more comprehensive understanding of motor skills development and a more effective strategy of preventing or confronting obesity and physical inactivity for educational and clinical practitioners.