The invention relates to a heat error measuring system of the whole workbench of a numerical control machine tool and a measuring method of the system. A positioning plate adsorbed by the surface of the workbench of the numerical control machine tool, the positioning plate is provided with multiple cuboid standard members uniformly, an I/O port of a PMC module of a numerical control system of the machine tool is connected with a signal converter, the signal converter is in bidirectional communication with a computer, a measuring head is mounted in a cutter position of the numerical control machine tool, and the cuboid standard members, the measuring head, the numerical control machine tool, the signal converter and the computer form the heat error measuring system. According to the invention, multi-point heat error measurement of the workbench of the numerical control machine tool can be realized via only one measuring head and multiple cuboid standard members, and the cost is low; and the signal converter is used to realize communication between the numerical control machine tool and the computer, data is measured and stored automatically, the required labor force of measurement is reduced substantially, and manual errors caused by manual measurement and manual data recording are avoided.