I'm using this switch and found that file transfer speed is dramatically drop while VPN is connected - 10.8MB/s vs. 2.7MB/s(vpn). Our RouterOS has been upgraded to Ver.2.9. Anyone can help me why this happened?

1. RouterOS on CSS326? Or are we talking about CRS326?
   And I highly doubt ROS is version 2.9, that's more likely SwitchOS 2.9.
   .
2. Where's the VPN endpoint running, on the same device? If we're talking about CRS and VPN is terminated on it, then ... CRS is a switch with low-end routing capabilities and one must not expect to see high routing/VPN/firewall performance.

All in all, I'm confused about your actual setup and where potential bottleneck might be.

I think I confused on router model, the Router Model is Mikrotek 2011iL, running RouterOS v6.43.8, firmware updated to 6.43.8. When using vpn on this device, we have problem that vpn speed is only 2.7MB/s vs 10.8MB/s. Same problem also happened on Mikrotek Cloud Router Switch CRS125, are these models suitable for VPN services? Please help, thank you.

2011 is a dated model, without hardware offloading for vpn...It will not break any speed records

You might get a bit more out of it: check if you have the right MTU set, so that there is no packet fragmentation.

750GR3 can be a good choice if you need 300Mbps IPS
ec VPN.

Or you can choose 3011/4011 rather than 2011/CRS , cause they have IPSec HW offload.

(If you don't have sensitive data that need to be encrypted, try pptp maybe have the better speed.)