Flowchart is commonly used diagram to represent the processes in design phase of a software system. However, the flowchart of a complex software system inevitably contains the nested structures of branching and looping of the processes. The verification of these nested structure of the flowchart in advance is still difficult to conduct even using simulation techniques. In this paper, we intend to consider the complex flowchart with nested structures, so called nested-if and nested-loop, as our input design model. A set of mapping rules is proposed to transform the input complex flowchart with nested structures into the hierarchical coloured Petri nets to avoid the drawing of a single huge net of complicate model. The hierarchical coloured Petri nets also provides us to manage level of abstraction of the formal model and helps us concentrate on only an appropriate detail at a time. In our transforming approach, both data flow and control flow of the processes in flowchart are concerned as well so that all changing states of the observable variables in the flowchart would be represented and simulated in our resulting hierarchical coloured Petri nets. The CPN simulation tool is used to test and ensure the correctness of our resulting hierarchical coloured Petri nets.