Shield tunneling prior to the shafts excavation is an efficient and economical method in the construction of the heat-supplying shield tunnel. Combining the first large cross-section heat-supplying shield tunnel project in China, the characteristics of the construction method are analyzed, and the control measures of segment joints deformation are put forward. Based on the site conditions, the numerical analysis model including interface element is established, and the control effect of the measures is analyzed and evaluated. Through on-site monitoring, the change law of longitudinal stress and joints deformation in different construction stages are measured. Based on the numerical analysis model, the effects of tunnel depth, stratum and grouting reinforcement area on joints deformation are analyzed. The results show that: the deformation of segment joints can be divided into two stages in the project of shield tunneling prior to the shafts excavation: shaft excavation and segments removal, and the segments removal is the main factor. According to the results of numerical calculation and on-site monitoring, the control measures of longitudinal tension lining and retightening bolt, priority to pouring concrete in the bottom of tunnel and secondary grouting behind lining can control the loss of longitudinal stress, and reduce the joints deformation. The maximum deformation of segment joints is 3.51 mm, which meets the waterproofing requirements of shield tunnels. In the project of shield tunneling prior to the shafts excavation, the deformation control of the top segment joints should be strengthened in the shallow tunnel, while for the deep tunnel, which should be strengthened of the bottom segment joints. When the tunnel passes through the stratum with larger resilience modulus, the deformation of the bottom joints will be larger. Grouting reinforcement of surrounding soil can reduce the loss of longitudinal stress and the joints deformation effectively.