The invention discloses a method and a system for charging a mobile data service. The method comprises the following steps that: when a user requests a new packet data protocol (PDP) service, a gateway GPRS (general packet radio service) support node (GGSN) triggers an on-line charging system (OCS) to charge an unbilled service flow which is generated by the user at present after determining that the PDP service is required to be charged on line according to the user request, distributes flow quota for the PDP service and notices the GGSN; and the GGSN monitors the using flow of the PDP service according to the current flow quota of each PDP service, triggers the OCS to charge the unbilled service flow which is generated by the user at present when the using flow of the PDP service reaches the flow quota, newly distributes the flow quota for the PDP service and notices the GGSN. By the method and the system, an operator is prevented from being unpaid, so the user can control consumption expenditure.