Linux is free and open source operating system whereas Windows is a commercial operating system whose source code is inaccessible.
Windows is not customizable as against Linux is customizable and a user can modify the code and can change its the look and feel.
Linux provides high security than windows because Linux is open source.
Windows must boot from the primary partition. In contrast, there is no such constraint in Linux it can be booted from either primary or logical partition.
The separation of the directories is done using a backslash in windows. On the contrary, in Linux, these are separated by using forward slash.
In Linux, file names are case sensitive while windows file name are case-insensitive.
Linux uses the monolithic kernel which consumes more running space whereas Windows uses the micro kernel which takes less space but system running efficiency is lower than Linux.