Choosing reasonable control measures for different intensity rockburst risks not only effectively prevents and mitigates rockburst risks but also reduces time and engineering investment costs. Due to the limitations of the tunnel boring machine’s structure and working conditions, tunnels excavated by TBMs are highly susceptible to rockbursts. What is even worse is that there are very few measures to control the rockburst risk in these tunnels. Implementing reasonable control measures from the limited mitigation measures to control and mitigate rockburst in TBM tunnels is an urgent problem that warrants a solution. In this paper, a large number of on-site rockburst risk control cases and a large amount of MS monitoring data (the total mileage of MS monitoring is approximately 7 km, lasting for 482 days) are used to derive a reasonable scheme to control the rockburst risk of different intensities in twin TBM tunnels. First, the rockburst early warning effect of the two headrace tunnels of the Neelum–Jhelum hydropower station based on microseismic monitoring is analyzed. Second, based on highly accurate rockburst warning results, 94 rockburst risk control cases are applied to analyze the control effect of different control measures at different intensities of rockburst risk. Then, by combining factors such as the time cost and expense cost of different control measures, more reasonable control measures for different intensity rockburst risks are proposed: for slight rockburst risk, normal excavation is preferred; for moderate rockburst risk, horizontal destress boreholes are preferred; and for intense rockburst risk, a combination of measures of shortening daily advance and horizontal destress boreholes is preferred. The research results can provide a reference for other TBM excavation projects to carry out rockburst risk prevention and mitigation.