After deep mining, the discontinuous deformation characteristics of roadway roofs become more and more obvious, resulting in the emergence of separation fractures in the rock mass, which seriously affects the stability of the roof rock mass. By taking the air return roadway 21204 (ARR 21204) in Hulusu Coal Mine as the engineering background, this article reveals the discontinuous deformation characteristics of deep buried roadway roofs through field research, numerical simulation, theoretical analysis and engineering practice. After roadway excavation, the rock masses in different shallow roof horizons show different degrees of stress unloading, resulting in the occurrence of discontinuous deformation phenomena in rock masses. With the rise of the roof rock horizon, the degree of discontinuous deformation fades away until a continuous deformation zone with small deformation and stable rock strata appears. In addition, with the increase in the roadway buried depth, the extent of the discontinuous deformation of the roof and its extended range tend to increase. In view of the discontinuous deformation control of the roof, the technology of linkage control of thick layer cross-boundary anchorage is proposed. By establishing the thick anchorage ring of the roof, the bolts cross the discontinuous deformation zone to support the stable rock strata in the deep continuous deformation zone, thereby realizing the linkage control of the large and small displacement of the rock masses in these two zones and limiting the progressive damage of the roof rock mass from shallow to deep. The industrial test shows that the scope of the separation fracture zone on the roof is controlled at the shallow stratum of 0.85 m due to the great decrease in the surface displacement of roadway, which effectively restricts the progressive upward extension of the discontinuous deformation zone of the roof. The research results can provide references for the safe and efficient control of roadway roofs under deep mining conditions.