Nintendo officially only supports memory cards up to 32GB -- no matter whether you're using SD or microSD cards and which 3DS iteration you own. There's no guarantee a larger one will work, though ...

The New Nintendo 3DS and 3DS XL use MicroSD Cards, unlike the original 3DS's standard size. The New Nintendo 3DS is officially compatible with anything from a 2GB microSD card up to a 32GB microSDHC ...