The invention discloses an embedded thermal error real-time compensation controller of a numerical control machine tool. The controller comprises a fiber bragg grating temperature sensor, an embedded processor, an FPGA chip, a thermal compensation execution module and a system power source. A thermal error half closed loop feed-forward compensation mode and a feedback pulse superposition compensation strategy are adopted, the fiber bragg grating temperature sensor is installed on the numerical control machine tool, and a BP neural network mathematical model embedded into the embedded processor is used for predicting the error value, which is generated by temperature changes, of the numerical control machine tool; the thermal error compensation execution module is inserted into a position feedback loop of the numerical control machine tool, and thermal error real-time compensation is achieved through superposing compensation pulses inside feedback pulses. The FPGA chip is adopted for generating the compensation pulses and implementing compensation, the frequency of the compensation pulses can meet the requirement for the high-speed machining state of the numerical control machine tool, and system real-time performance is improved.