In this paper, the observer-based output consensus of leader-following fractional-order heterogeneous nonlinear multi-agent systems with potentially different state dimensions and different dynamics are investigated. Considering the agents' states may be not available in practice, the distributed state observer is designed for each agent. Then corresponding distributed control protocols based a proposed virtual exosystem are proposed to convert the output consensus problem into the stabilisation problem. By employing matrix theory, algebraic graph theory and the stability theory of fractional system, the state consensus of the virtual exosystem and the output consensus of heterogenous fractional nonlinear MAS is achieved. Moreover, the sufficient conditions are also obtained. Simulation examples are presented to verify the effectiveness of the main results.