The best start would probably be both parts of Windows Internals:

https://www.amazon.com/Windows-Internals-Part-architecture-m...

https://www.amazon.com/Windows-Internals-Part-Developer-Refe...

These aren't about programming per se, but if you want to do systems programming it helps to have a detailed understanding of the system. :)

After that, specific reading probably depends on the exact task you want to perform, but MS has good documentation and tutorials in many areas. Writing drivers, for example:

https://docs.microsoft.com/en-us/windows-hardware/drivers/ge...