Abstract-Three-dimensional, physics-based simulators are important to the field of self-reconfigurable robotics because they allow researchers to approximate the physical interactions and autonomous behaviors of large numbers of modules in a low-cost, safe, and highly-controlled manner. This paper presents a novel, high-performance, general-purpose simulator for autonomous, self-reconfigurable robots called ReMod3D (RM3D) that overcomes the speed and scalability limitations of existing self-reconfigurable simulators while, at the same time, allowing for realistic module structures, complex environments, and high physical simulation fidelity. While most existing selfreconfigurable simulators view modules as actuated physical bodies with programmable controllers, RM3D views them as embodied agents, defined not only by their physical bodies (links, joints, docks, sensors, actuators) but also by their minds (actions, percepts, behaviors, world models) and the noise inherent in the interaction between sensors, actuators, and the environment. RM3D also simulates inter-module dock connection breakage, something novel for self-reconfigurable robot simulators. Additionally, we present experimental evidence showing that this novel architecture makes RM3D well-suited to locomotion, manipulation, reconfiguration, and embodied intelligence research.