A facile and controllable method is developed to encapsulate phase change material (PCM) with biocompatible and non-toxic calcium alginate as the shell material. The PCM capsules are successfully prepared by using a simple co-extrusion minifluidic device with melted paraffin wax Rubitherm RT27 as the inner fluid and sodium alginate solution as the outer fluid, and the capsules are collected in a container with CaCl2 solution. In the whole preparation process, all the chemicals used to form the capsule shells are biocompatible and non-toxic. The prepared PCM capsules are featured with spherical shapes, highly monodisperse sizes and perfect core–shell microstructures. The capsule diameter and the RT27 content in the capsules as well as the resultant thermo-regulating capacity of the PCM capsules can be precisely controlled by simply adjusting the inner and outer flow rates. The results show that it is more effective to adjust the capsule diameter as well as the RT27 content inside PCM capsules by varying the inner flow rate rather than the outer flow rate. With increasing the inner flow rate but fixed outer flow rate, the diameters of both wet and dried capsules as well as the RT27 content inside the PCM capsule increase linearly. With increasing the outer flow rate but fixed inner flow rate, the average diameter of wet capsules slightly increases linearly but that of dried capsules nearly does not change, while the RT27 content inside the PCM capsule slightly decreases gradually. The proposed method for the encapsulation of PCMs is mild, simple, controllable, and easy to be scaled up. The prepared PCM capsules exhibit good thermo-regulating ability as well as satisfactory stability and reproducibility, and are highly attractive for various thermo-regulating, energy-storing and energy-saving applications.