Real-life control tasks involve matter of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been developed to model the dynamics of these complex scenes; however, relying on approximation techniques, their simulation often deviates from real world physics, especially in the long term. In this paper, we propose to learn a particle-based simulator for complex control tasks. Combining learning with particle-based systems brings in two major benefits: first, the learned simulator, just like other particle-based systems, acts widely on objects of different materials; second, the particle-based representation poses strong inductive bias for learning: particles of the same type have the same dynamics within. This enables the model to quickly adapt to new environments of unknown dynamics within a few observations. Using the learned simulator, robots have achieved success in complex manipulation tasks, such as manipulating fluids and deformable foam. The effectiveness of our method has also been demonstrated in real world. Our study helps lay the foundation for robot learning of dynamic scenes with particle-based representations.