Modularized programming has many advantages. However, the current encapsulation makes a hard partition between modules. It is weak in communication. In this paper, a layered programming paradigm is presented, where "layer" is an abstract interface to support functional partitioning. Under this paradigm, all instantiated modules are automatically connected to a thread network, which provide a platform for communication. Protocols are defined to coordinate the behaviours between them and control mechanisms, such as concurrency, parallelism, distribution and pipeline, etc. An implementation is presented to show the effectiveness of protocol programming.