What is the difference

phyiscal size is different,

matx is roughly 9 in by 9 in and atx is 9 in by 12 in.

matx is usually cheaper, and offers less available pci-e slot and other internal connectors

atx has more physical pci-e slots, the 16x pci-e slot are more spread out, in case you have a dual or tri slot graphic cards, sometimes, the pcie slots are not accessible.

in terms of cpu/mem support as well as cpu overclockability, matx and atx of the same line up is usually identical.
 

Ok, usually that's the first thing they change but in this case it isn't.

A quick glance between the two is the amount of pci-e slots and the amount of USB ports.