There are several file systems employed by both operating systems, thus you need to be more specific when asking for a comparison. Windows most commonly uses NTFS these days, although older versions used FAT. There are several popular file systems for Linux, depending on usage. The most common is ext3 or ext4, although ext2, ReiserFS, JFS, XFS, and several others all have fairly common usage.
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Windows only supports file systems such as FAT, exFAT, and NTFS.
Linux has a wide variety of file systems that depends on distributions and the file system, may be officially or unofficially supported. For the most part, you can be sure that EXT2/3/4 are supported at the minimum and anything else extra you will need to refer to the documentation (for filesystems like ReiserFS, XFS, JFS, ZFS, or BtrFS). It also do support FAT for compatibility, and for platform-specific file systems like NTFS or HFS/HFS+ are at the bare minimum.