This paper introduces the concept of a virtual ecosystem and reports the following three mathematical approaches that could be widely used to construct such an ecosystem, along with examples: (1) a molecular dynamics simulation approach for animal flocking behavior, (2) a stochastic lattice model approach for termite colony behavior, and (3) a rule-based cellular automata approach for biofilm growth. The ecosystem considered in this study consists of artificial organisms and their environment. Each organism in the ecosystem is an agent that interacts autonomously with the dynamic environment, including the other organisms within it. The three types of model were successful to account for each corresponding ecosystem. In order to accurately mimic a natural ecosystem, a virtual ecosystem needs to take many ecological variables into account. However, doing so is likely to introduce excess complexity and nonlinearity in the analysis of the virtual ecosystem's dynamics. Nonetheless, the development of a virtual ecosystem is important, because it can provide possible explanations for various phenomena such as environmental disturbances and disasters, and can also give insights into ecological functions from an individual to a community level from a synthetic viewpoint. As an example of how lower and higher levels in an ecosystem can be connected, this paper also briefly discusses the application of the second model to the simulation of a termite ecosystem and the influence of climate change on the termite ecosystem.