Autogenous shrinkage is the volume deformation of a closed, isothermal, cementitious material system not subjected to external forces. How to accurately predict the autogenous shrinkage in hardening cement-based materials is an important issue in concrete technology because autogenous shrinkage increases cracking risk and reduces the durability and service life of reinforced concrete structures. Many models simulated the autogenous shrinkage of cement-based materials based on some mechanisms such as capillary pressure and disjoining pressure. These models are normally empirical and cannot reveal the deformation behavior of cement-based materials under the internal load of the driving force of autogenous shrinkage in microscale. As a consequence, the reliability of these models are questionable. This paper proposes a numerical model to simulate the autogenous shrinkage of hardening cement paste. A cement hydration and microstructure model HYMOSTRUC3D is used to simulate the microstructure of cement paste. A pore morphology based method is applied to describe the water and empty capillary pores distribution in the microstructure. Capillary pressure in the microstructure of cement paste is calculated from relative humidity measured by experiment based on Kelvin equation. A discrete algorithm is proposed to divide the hydration time into several static times. At each static time, a lattice finite element fracture method is used to simulate the deformation of simulated microstructure of cement paste under capillary pressure imposing. The autogenous shrinkage of hardening cement paste is equal to the sum of deformation of cement paste at each static time. The autogenous shrinkage of Portland cement paste with water to cement ratio of 0.3 is predicted. The simulation results are in a good agreement with experiments.@en