Advances in experimental instrumentation and automation generate increasingly rich datasets, but turning experimental observations into microscopic understanding remains a bottleneck in scientific discovery. To accelerate this process, we introduce AI Theorist, a system of artificial intelligence (AI) agents for autonomous discovery of physical models through hypothesis generation, first-principles calculations and evidence-driven refinement. We apply the framework to α-RuCl₃, a leading candidate material for realizing a Kitaev quantum spin liquid, to investigate its electronic structure through optical spectra. AI Theorist develops a new interpretation of the optical and photocurrent observations, identifying distinct excitonic states with contrasting optical selection rules and real-space distributions. To our knowledge, this is the first demonstration of an AI system autonomously developing a physical model to explain previously unpublished experimental observations in a quantum material, utilizing first-principles electronic-structure and many-body calculations. Our results establish a route to autonomous theoretical discovery in materials science, in which AI agents use first-principles calculations to turn experimental observations into physical models and testable predictions.