Linux and Windows are both hot points in the academic field of computer technology. The interoperability of them two further expands their respective development area. On the other hand, some new technology problems are also produced. Focusing on the interoperability of Linux and Windows in desktop domain, this paper goes into a little more detail about these problems and their solutions. In desktop domain, the two operating systems can mutually run programs by adopting virtualization technologies such as API emulation or by altering source codes of operating systems, can mutually deal with data files by adopting open, common and unified data file format standards, and can mutually access file systems by adopting the mechanism of file system in kernel space or in user space.