To research the coupling effect of construction sequence and soil chamber pressure, as well as the subgrade micro-deformation control during the process of shield tunneling under railway subgrades, the earth pressure balance (EPB) shield of Harbin Rail Transit Line 3 passing under multiple railway tracks, including the Harbin-Mudanjiang High-Speed Railway, was taken as the background. Methods such as numerical simulation, theoretical calculation, and on-site measurement were adopted to investigate the influence of different construction sequences of double-line tunnels and soil chamber pressure settings on stratum deformation. The numerical results show that when two EPB shields advancing towards each other meet directly below the railway subgrade, the settlement increases by 0.4 mm compared with meeting on both sides, with an increase rate of 12.86%. When the soil chamber pressure is set to 220, 200, and 180 kPa, the maximum settlements are 3.50, 5.14, and 7.92 mm, respectively. The correlation analysis of on-site tunneling parameters reveals that the ratio of screw conveyor rotating speed to tunneling speed is negatively correlated with soil chamber pressure, with a Pearson correlation coefficient of -0.49. The specific speed value of this stratum should be controlled at 90.98 r/m, and the fluctuation of soil chamber pressure should range from -20 kPa to 25 kPa. When the Rankine earth pressure at rest plus a 20 kPa reserve pressure (to offset pressure fluctuations) is used as the calculated value of soil chamber pressure, the measured values (196-227 kPa) after controlling the specific speed value are in good agreement with the formula-calculated values (180-222 kPa). By using the tunnel monitoring and early warning platform to monitor the settlement rate and cumulative settlement in real time, and adjust in time based on feedback, the final settlement of the railway subgrade is controlled at 3.41 mm, which meets the safety requirement of not exceeding 6 mm.