nios ide in windows and linux are different?

The newest version of NiosII EDS includes NiosII SBTE(Software Build Tool for Eclipse) which uses BSP project, while also supports the previous NiosII IDE which uses syslib project. You can look at these from Altera Homepage.

The new NiosII SBTE is more convenient because it can view the HAL code directly. That's a very easy-to-use function from my opinion. But there are also some important differences betwwen them.

The new version uses NiosII SBTE by default, but you can also open NiosII IDE from StartMenu in Windows. In Linux, the command "nios2-ide" uses for opening NiosII IDE, while the command "eclipse-nios2" opens NiosII SBTE. The two commands both locates in "[installation directory]/nios2eds/bin".