A method and user equipment (UE) for obtaining power headroom information in a communication system are provided. The method includes acquiring information for a path loss reference, wherein the information for the path loss reference indicates whether the UE applies as the path loss reference either a downlink of a primary cell or a downlink of a secondary cell (SCell), triggering a power headroom report (PHR) if a path loss is changed more than a threshold for at least one activated cell which is used as the path loss reference, obtaining power headroom information for each activated cell, if extended PHR is used and an uplink resource is allocated for new transmission, and generating a medium access control (MAC) protocol data unit (PDU) including the power headroom information for each activated cell and an indicator for each activated cell. The indicator indicates whether power headroom information is based on a real physical uplink shared channel (PUSCH) transmission or a PUSCH reference format.