The applications of heterogeneous embedded systems for biomedical engineering are promising, as quick response of biomedical systems is often required due to the life-saving nature of biomedical engineering, and multiple devices with completely different cores and designs can be involved in a single patient. In this paper, we propose a multiprocessing framework and then, with regard to the framework, we propose an architecture for heterogeneous embedded systems that uses finite state machines (FSMs). A multithreading method on an electrocardiogram (ECG) software is implemented as the verification of our framework.