The invention discloses a planar array electrical capacitance tomography method and a system thereof, and relates to the technical field of image reconstruction. In the invention, the planar array electrical capacitance tomography system comprises a capacitance sensor, a data measurement and acquisition module and a computer. The capacitance sensor converts the distribution of the substance-fieldmedium of the object detected to a capacitance value; the data measurement and acquisition module is used for measuring and acquiring the capacitance value between any two electrode plates, and transmitting the measured capacitance data to the computer; the computer optimizes the capacitance data through fuzzy C-mean clustering algorithm, uses the optimized capacitance value as an image reconstruction value, reconstructs the defect image in combination with a non-iterative image processing algorithm or an iterative image processing algorithm, and obtains a reconstructed image. Compared to conventional imaging methods, the planar array electrical capacitance tomography method and the system thereof can solve the problem that the capacitance data is influenced by the position of the electrode plates and the noise interference of the detection environment, and obtain more stable and high-quality image of the measured field.