The invention discloses an input virtual terminal management method and system. The method comprises the steps as follows: an input data set is established in the preset position; identification information of effective input virtual terminals under LNs (logical nodes) is acquired; and the identification information serving as elements of the input data set is added into the input data set. Therefore, through the process, input virtual terminals which are not effective virtual terminals are excluded from the input data set; and all identification information in the input data set is the identification information of the effective input virtual terminals under the LNs, so that the identification information in the input data set is directly positioned to corresponding input virtual terminals with the input data set serving as a reference during the process of following virtual terminal connection configuration and the engineering development of an intelligent substation. In conclusion, with the adoption of the input virtual terminal management method and system, the centralized management for the effective input virtual terminals is realized, and various problems caused due to absence of a centralized management method of the input virtual terminals in the prior art are solved.