<p>The damage of marine soft clay during the loading process is closely related to the microstructure changes. Triaxial shear tests and field emission scanning electron microscope (FESEM) tests were carried out on the marine soft clay in the fourth layer of Shanghai. It focuses on analyzing the effect of microscopic clay aggregates break-up on the damage of Shanghai marine soft clay during the shearing process, and revealing the damage mechanism. The results show that: during the shear process, the Shanghai marine soft clay stress–strain curves show obvious strain hardening phenomenon, and the secant modulus undergoes attenuation, and the maximum attenuation degree reaches 90.9%. The microstructure mainly undergoes clay aggregate cementation destruction, clay aggregate break-up and disintegration into smaller aggregates or dispersed clay particles. The relative breakage <i>Br</i> of clay aggregates increases gradually with the increase of confining pressure and strain, with a maximum value of 0.24. It can be calculate by the proposed equation with confining pressure and strain. The damage variable <i>D</i> is proposed based on the relative breakage <i>Br</i>, the <i>D</i> has a negative exponential relationship with strain. And the secant modulus damage evolution equation of Shanghai marine soft clay is developed, which can accurately describe the modulus damage evolution of Shanghai marine soft clay in the shear process. It can further deepen the understanding of the damage of Shanghai marine soft clay.</p> Graphical Abstract <p></p>