Because traditional Linux distribution has the problem of complicated drivers, graphical desktop of extreme resource consuming and excess software, we build a system which is optimized for a particular processor. Using GNU(GNU's Not UNIX) tool chain, Linux 2.6.25 kernel and related components we propose a micro system solution in USB storage devices. In the process of building the tool chain, confusing compile order has been marked and explained. We have a detailed discussion of establishing cross-compiler environment and the use of the toolchain. The solutions of root permissions, the kernel USB related module selection, and grub boot failure are elaborated. This solution, based on the host system of opensuse 11.4 and the open source, has achieved the purpose of completing the Linux system development in x86 PC and USB flash disk. The result shows that in the low-cost test bench the system takes about 600 MByte of storage space, provides a complete teaching programming requirement, and ensures faster start-up and operation rate.