how to limit the size of each sub-domains?

Only the account itself is limited by disk quota and bandwidth size. Subdomains do not have such limits other than possibly limiting the number of subdomains that can be created.

If you need the subdomains to have limits, they would need to be separate accounts owned by a reseller user who then puts each subdomain account into a package with limits.

If you feel having each individual domain (addon domain) or parked domain with limits would be a necessary feature, you may wish to make a request at Feature Requests for cPanel/WHM

Thanks!