The inherent properties of soft coal seams and their mechanical environment make long boreholes susceptible to issues like collapse, deformation, and blockages. These problems shorten the service life of the boreholes and hinder extraction efficiency. This paper tackles these challenges by analyzing the deformation and damage patterns of long boreholes in soft coal seams. It examines the stress distribution and deformation characteristics around both protected and unprotected boreholes at different burial depths. Additionally, it recommends using screen pipe protection technology to improve gas extraction and mining operations, as demonstrated in Changping Coal Mine. The results show that screen pipe protection substantially improves the stress distribution and deformation stability of coal seam boreholes. The flow attenuation coefficients of two boreholes equipped with protection technology decreased by 48% and 61%. After 50 days of extraction from boreholes with a protection rate exceeding 90%, gas concentration remained above 50%, which is 2.59 times higher than that of unprotected boreholes. This technology effectively addresses the frequent accidents, poor extraction performance, and inefficiency of long boreholes in soft coal seams, ensuring the mine’s safe and efficient production.