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Generally speaking, MDT is suitable for small-scale environments, while SCCM is more suitable for large-scale environments.
1.MDT is free, which is a huge advantage for many smaller business. MDT as a standalone tool is great for tiny environments without a lot of computers to migrate. MDT is also a fine fit for environments that are not connected. MDT is best used for creating "thin" images that just contain OS updates and runtimes. It is Lite Touch Installation (LTI), not fully automated. MDT is primarily used for image computers and storing images, customizing them, etc.
2.SCCM's license costs are also much more than those of MDT, as MDT is free. SCCM on the other hand, is a much more complex tool which allows you to do a lot more than MDT does. Whereas SCCM is best used for creating "thick" images containing line-of-business applications. It can also incorporate WSUS within it, and provide update reporting. It can also provide auditing against what a standard machine should be.
3.If you are in a very big organization, you can integrate MDT with SCCM. More specifically, if you have thousands of computers and many different applications to manage it’s a good direction to consider. You should integrate MDT operating system images with Configuration Manager for large-scale operating system deployments to take advantage of enterprise-level management features such as: replication, multicast DPs, bandwidth management, reporting, poor network connections to remote sites, and stronger security through encryption and password protection. The SCCM plus MDT combination is preferred for "zero touch installations" and "user driven installation deployments".
Please refer to: Microsoft Publishes Best Practices for Windows Deployments
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