Software programming is often considered to be difficult for many engineering students. Nowadays, many control and automation systems are facing the increasingly sophisticated functional and non-functional demands. In such systems, software portion is always expected to have the greater impact. Therefore, educators continue to face great challenges in getting students to be capable of conducting efficient software development. In the last decade, modelbased design (MBD) is an emerging development methodology for modern software. Its efficiency has been demonstrated in large scale software engineering projects. This paper presents our experience of integrating modern MBD concepts and tools into a Programming Tools (PT) course. First, the basic components in the MBD process are exposed to students, especially its two unique components -automated code generation and model-based verification and validation (V&V). Second, three modeling languages: Matlab/Simulink, LabVIEW and SCADE are exposed to students. They all have been widely applied in embedded control and automation domains. Third, input programming languages of these selected tools are introduced to students to help them apply the tools in the laboratory assignments and class project.