Recently, there has been a clear trend towards the application of ad hoc networking technology in civil aviation communication systems, giving birth to a new research field, namely, aeronautical ad hoc networks (AANETs). An AANET is a special type of ad hoc wireless network with a significantly larger scale and distinct characteristics of its mobile nodes. Thus, there is an urgent need to develop a simulator to facilitate the research in these networks. In this paper, we present a network simulator, Aero-Sim, for AANETs. Aero-Sim, which is based on the freely distributed NS-2 simulator, enables detailed packet-level simulations of protocols at the MAC, link, network, transport, and application layers by composing simulations with existing modules and protocols in NS-2. Moreover, Aero-Sim supports three-dimensional network deployment. Through several case studies using realistic China domestic air traffic, we show that the proposed simulator can be used to simulate AANETs and can reproduce the real world with high fidelity.