To investigate the effect of calcium carbonate whiskers on the shrinkage properties of cement paste, dry shrinkage, chemical shrinkage and autogenous shrinkage of specimens with three kinds of water cement ratios were tested at different ages, respectively. The phase composition and pore structure changes of the autogenous shrinkage specimens were characterized using X-ray diffraction (XRD) and mercury intrusion porosimetry (MIP), respectively. The results show that calcium carbonate whiskers have the characteristics of adsorbing and transferring free water in cementitious materials. Under different water cement ratios, calcium carbonate whiskers exhibit different effects on drying shrinkage, and the degree of influence shows a trend of initially increasing and then decreasing with the dosage of calcium carbonate whiskers. The chemical shrinkage shows a tendency of increasing and then decreasing with its dosage. Calcium carbonate whiskers can significantly improve the self-shrinkage, especially the early autogenous shrinkage, and the increase of the water cement ratio makes the improvement of the early autogenous shrinkage by calcium carbonate whiskers more significant. The whiskers refine the pore structure without generating new hydration products.