Waste marine clay, a commonly found natural deposit in coastal regions, can serve as partial cement alternative in mortar after thermal treatment, thus facilitate sustainable urban development without polluting the environment. This paper studied the influence of calcination temperature, fineness of grounded particles and cement replacement ratio on the pozzolanic activity of the thermally treated marine clay. TG results reveal that dehydroxylation of waste marine clay with low kaolinite mainly occurs between 500 and 600 °C and completes at 700 °C. Calcined marine clay accelerates cement hydration and causes higher total heat. From the microscopic analysis, it can be found that the calcined marine clay favours the consumption of portlandite accompanied by the formation of the C–S–H, C-A-H, AFm and strätlingite. MIP results show that calcined marine clay can refine the pore system with declines in the threshold pore size, critical pore size and average pore size, while the total pore volume and porosity are increased with higher replacement ratio. Mortar incorporating 15% fine calcined marine clay as cement substitute exhibits comparable strength with the reference mortar. However, beyond 45% cement replacement ratio, mortar strength substantially drops as a result of cement dilution effect, porous structure and agglomeration of marine clay.