This paper deals with the problem of secure communication based on Multi-Input Multi-Output (MIMO) chaotic systems. Single input secure communication based on chaos can be easily extended to multiple ones by some combinations technologies, however all the combined inputs possess the same risk to be broken. In order to reduce this risk, a new secure communication scheme based on chaos with MIMO is discussed in this paper. Moreover, since the amplitude of messages in traditional schemes is limited because it would affect the quality of synchronization, the proposed scheme is also improved into an amplitude-independent one.