Covert channels are widely considered as a major risk of information leakage in various operating systems, such as desktop, cloud, and mobile systems. The existing works of modeling covert channels have mainly focused on using finite state machines (FSMs) and their transforms to describe the process of covert channel transmission. However, a FSM is rather an abstract model, where information about the shared resource, synchronization, and encoding/decoding cannot be presented in the model, making it difficult for researchers to realize and analyze the covert channels. In this paper, we use the high-level Petri Nets (HLPN) to model the structural and behavioral properties of covert channels. We use the HLPN to model the classic covert channel protocol. Moreover, the results from the analysis of the HLPN model are used to highlight the major shortcomings and interferences in the protocol. Furthermore, we propose two new covert channel models, namely: (a) two channel transmission protocol (TCTP) model and (b) self-adaptive protocol (SAP) model. The TCTP model circumvents the mutual inferences in encoding and synchronization operations; whereas the SAP model uses sleeping time and redundancy check to ensure correct transmission in an environment with strong noise. To demonstrate the correctness and usability of our proposed models in heterogeneous environments, we implement the TCTP and SAP in three different systems: (a) Linux, (b) Xen, and (c) Fiasco. OC. Our implementation also indicates the practicability of the models in heterogeneous, scalable and flexible environments.