Autonomous systems underpinned by cognitive intelligence represent advanced forms of artificial intelligence studied in intelligence science, systems science, and computational intelligence. Traditional theories and technologies of autonomous systems put emphases on humansystem interactions and humans in-the-loop. This paper explores the intelligence and system foundations of autonomous systems. It focuses on what structural and behavioral properties constitute the intelligence power of autonomous systems. It explains how system intelligence aggregates from reflexive, imperative, adaptive intelligence to autonomous and cognitive intelligence. A Hierarchical Intelligence Model (HIM) is introduced to elaborate the evolution of human and syste...