The correct ambiguity resolution between reference stations is the core issue of the whole Network Real-Time Kinematic (RTK) technology. Aimed at long fixed time and low reliability of the low elevation angle satellite ambiguity resolution during the initialisation of the Network RTK system, a three-step algorithm is proposed in this paper. Firstly, the double difference wide-lane ambiguities are fixed on the basis of the Melbourne-Wubbena (MW) method. Secondly, the double difference L1 carrier phase ambiguities of the high elevation angle satellites are fixed rapidly based on the ionosphere-free combination model. Thirdly, the corresponding ambiguities of the satellites with low elevation angles are solved with restrictions from the double difference tropospheric information, which is obtained from observations of the high elevation angle satellites. Based on this algorithm, an overall scheme of the ambiguity resolution during the initialisation process of the Network RTK system is designed. Results from Global Positioning System (GPS)/Globalnaya Navigatsionnaya Sputnikovaya Sistema (GLONASS) data demonstrate that the three-step algorithm can reduce the ill-posed problems of the observation model effectively. Moreover, the speed and accuracy performances of the ambiguity resolution for the low elevation angle satellites using the proposed algorithm are better than those of the conventional method.