Is there anyway to set Quota for users in Fortigate ?

I think you need to be more specific, and to list which model of FortiGate and version of FortiOS you're running.

You also need to list out what sort of clients these are and how they are authenticated -- for instance, all local clients with no separate authentication, clients authenticated through a captive portal, clients authenticated to a separate authentication server (RADIUS, LDAP, AD), SSL VPN clients, IPSec VPN clients, etc.

A few thoughts and suggestions:

Do you want to set a quota for particular types of internet access by time or bandwidth?  If so, the proxy-mode version of Web Filters lets you specify time or bandwidth quotas for categories of web access.  Note that this is only the proxy mode version.  If you're running flow mode this isn't available.

If you're trying to limit users (by IP) to just a certain low level of bandwidth, look at traffic shapers.

If you're trying to limit per-user access by time or bandwidth where they are cut off once their limit is exceeded that's more complicated, and not something I've done.  If your users are authenticating through a captive portal or authentication server (RADIUS, LAPD, or AD) I think you can set various fields to control this.  Try taking a look at the CLI docs for:

config user setting   auth-timeout

  auth-timeout-type

  radius-ses-timeout-act

config user group

  edit GroupName

    set authtimeout (or auth-timeout?)

Hopefully that gives you some ideas to get you going.  If not, I'd come back with a more specific question about your situation.