We certainly see that some of
.exe file to executed but what the different functionality of the MSI files?
MSI is acronym for Microsoft Silent Installer, it runs .exe installer in background.
It is used in GPO, for example if you want to deploy an application on a Windows Infrastructure you are managing, You have to create a new GPO rule with the MSI and the MSI will be installed on every machine without user intervention needed.
GPO being "Group Policy Object" which "provides the centralized management and configuration of operating systems, applications, and users' settings in an Active Directory environment."