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.