Abstract Shale gas exploration and development maintained good momentum, but it has some problems at the same time urgently need to be solved, such as sustained casing pressure (SCP), which brought a lot of safety issues and shortened the well service lifetime. A series of experimental investigations and numerical studies were carried out to analyze the development of the micro-annulus width of the second interface in the casing-cement sheath-formation assembly before and after using the pre-stressed cementing technology. Triaxial compression tests computed tomography scanning and accumulated plastic strain tests were conducted to evaluate the residual strain under the combined action of cyclic loading-unloading and confining pressure. Full-size cement sheath experiments were performed to quantify the width critical value of the micro-annulus when gas leakage began during multistage fracturing. The corresponding numerical models of the full-size cement sheath physical simulation facility and pre-stressed cementing technology of a real deep shale gas well were developed. Different combinations of factors were analyzed to quantify the variation of micro-annulus and tolerance ability of fracturing section numbers. The influence of a series of factors, including casing inner pressure, pre-stressed loading, and mechanical parameters of the cement sheath, were analyzed. The result of the research showed that the reduction of casing pressure and increase of pre-stressed loading could help to maintain the seal integrity of the cement sheath. Micro-annulus risks can be reduced through lowering elasticity modulus and raising Poisson's ratio. Eight deep horizontal shale gas wells were cemented with pre-stressed loading. The practical application results showed there was no SCP in prior and post-multi-stage fracturing, which proved the effectiveness of this method.