Boring Trepanning Association (BTA) deep hole drilling is widely used in machining tube sheet of steam generator. In order to get a better service integrity, the surface quality after machining is required to be higher. In this paper, the effect mechanism of BTA deep hole drilling on the integrity and quality of the machined surface layer of low alloy steel SA508Gr.3Cl.2 for nuclear power are investigated. The results show that the gradient microstructure can be obtained by BTA drilling on the surface of inner hole, including the recrystallized layer with grain re nement and the plastic deformation layer with high density sub-crystal structure and grain distortion. With the increase of drilling speed and feed rate, the deformation layer thickness will increase. The proportion of low angle grain boundaries (LAGBs) increases with the increase of the depth from the machined surface under each drilling parameter. The increase of drilling speed leads to the increase of recrystallization degree and the proportion of LAGBs in the machined surface. The effect of feed rate on the proportion of LAGBs is opposite. The machined surface is characterized by regular peak and valley, and there are typical surface defects mainly involving feed marks, surface tearing, and ploughing grooves. With the increase of drilling speed, the surface roughness will decrease. The effect of feed rate on surface roughness is obviously lower than that of drilling speed. With the increase of drilling speed and feed rate, the depth of hardened layer increases gradually, which is caused by dislocation strengthening and ne grain strengthening effect during BTA drilling process. Higher drilling speed is recommended in forming a good machined surface with a strengthening layer of a certain thickness.