This paper presents a new method of modelling automation systems based on the combination and mutual transformation of Function Blocks of IEC 61499 and MATLAB Simulink/Stateflow. The ultimate goal of this development is to have a fully automated transformation between models built in the two platforms. The reasons for such transformation are due to the need for a proper validation environment for Function Blocks models and the difficulty in obtaining industrial acceptance in this new design approach. MATLAB Simulink/Stateflow provides a nice environment for modelling and simulation of control and embedded systems. Function Blocks are good for designing control application for complex physically distributed systems. An integrated software environment with transformation ability between these two tools will lead to a solution for the validation need for Function Blocks and also the adoption problems. This paper demonstrates a transformation practice where a Simulink model is transformed into a Function Block model in FBDK. The transformed model still requires some manual modifications to be executed because of the missing algorithm translation from MATLAB language to a language that can be used for algorithms in Function Blocks. This paper also discusses important issues of model transformation, such as semantics mapping, data type mappings and transformation rules