For application system based on single-chip microcomputer (SCM), software design becomes more and more difficult than hardware design. Most of the college students can scheme out hardware circuits, but seldom of them can write out high-quality code for comprehensive system. Thinking and methodology are the key factors deciding the code quality. This article analyzes current situation of programming teaching for SCM, then discusses the particularity of thinking and methodology for SCM programming. The teaching contents were reformed by introducing new thinking and methodology. The applications of new thoughts and methods were demonstrated by three examples: multi-petal structure, key-jitter elimination without time-consuming and programming method based on messages. The practice showed that the teaching reform expanded the students’ thinking and improved their capabilities to write high-quality programs.