Does anyone know how to configure inter-vlan routing on CRS 3XXX.
Yes, you just add them. If they were only connected on a switch they wouldn’t be able to communicate. Because they are on a router, they can. So you actually would need to block the InterVLAN routing at the switch if you didn’t want them to communicate.
https://wiki.mikrotik.com/wiki/Manual:Interface/VLAN#InterVLAN_routing