Development of a robust method for the preparation of cell aggregates with different shapes is one of the urgent requirements in tissue engineering, since they can be used as building blocks to mimic complex architectures in tissues. Herein, we describe a microfluidic droplet-based approach that can easily produce different shapes of cell aggregates in Ca-alginate microparticles by changing alginate and CaCl₂ concentrations. Using this approach, human cervical carcinoma, human hepatocellular liver carcinoma and human umbilical vein endothelial cell aggregates with spherical, spindle- and branch-like shapes were successfully obtained in a repeatable and controllable manner. Cytoskeletal analysis and SEM observation showed that the cell aggregates were densely packed and interconnected. Cell viability assays showed that the viabilities of the retrieved cells from the Ca-alginate microparticles were all more than 95% with good morphology and proliferation ability. Study on the formation mechanism revealed that the shape and size of the cell aggregates were mainly decided by the inner structures of Ca-alginate microparticles, which can be controlled by regulating their preparation conditions. This approach may possess great potential for the construction of various building blocks in tissue engineering with simplicity, controllability, applicability and practicality.