Deep space communication has its own features such as long propagation delays, heavy noise, asymmetric link rates, and intermittent connectivity in space, therefore TCP/IP protocol cannot perform as well as it does in terrestrial communications. Accordingly, the Consultative Committee for Space Data Systems (CCSDS) developed CCSDS File Delivery Protocol (CFDP), which sets standards of efficient file delivery service capable of transferring files to and from mass memory located in the space segment. In CFDP, four optional acknowledge modes are supported to make the communication more reliable. In this paper, we gave a general introduction of typical communication process in CFDP and analysis of its four Negative Acknowledgement (NAK) modes on the respect of file delivery delay and times of retransmission. We found out that despite the shortest file delivery delay, immediate NAK mode suffers from the problem that frequent retransmission may probably lead to network congestion. Thus, we proposed a new mode, the error counter-based NAK mode. By simulation of the case focused on the link between a deep space probe on Mars and a terrestrial station on Earth, we concluded that error counter-based NAK mode has successfully reduced the retransmission times at negligible cost of certain amount of file delivery delay.