My GSTR-2B shows less ITC than my purchase register. Which one do I claim in GSTR-3B?

Claim the ITC that appears in GSTR-2B, not the full figure in your purchase register. Under Section 16(2) of the CGST Act and Rule 36(4), credit is allowed only for invoices that are reflected in your GSTR-2B, so the register total is only a starting point for reconciliation.

For the difference, check why each invoice is missing: the supplier may not have filed GSTR-1 yet, may have reported it in a later period, or used a wrong GSTIN or invoice number. Follow up with the supplier. Once the invoice shows up in a later GSTR-2B you can claim it then, provided you are within the time limit in Section 16(4). Also exclude credit that is blocked under Section 17(5), even if it appears in GSTR-2B.

Keep the reconciliation on file, and confirm tricky cases with your CA.