3D Secure is an extra security step for the cardholder to authorise a payment before the transaction takes place.  

When payment is put through on a credit card activated with 3D secure, the bank that issued the card will request the cardholder to insert a  password/PIN.

3D Secure authenticates card holder identity, before handing on the card details to the payment gateway for deduction. The money will only be deducted from the card once the bank identifies the cardholder.