The invention discloses an intelligent control system of a double-field of view thermal imager. The intelligent control system comprises an infrared lens, a thermal imaging detector, a microprocessor, a stepping motor and a limit switch. The intelligent control system is characterized in that the microprocessor drives the stepping motor to operate through a motor driving circuit, and the input end of the microprocessor is connected with a photoelectric encoder and a temperature sensor. A control method of the intelligent control system of the double-field of view thermal imager comprises the steps of (a) detecting states, (b) moving to a starting position, (c) determining the distance of a large field of view, (d) moving to the position of the large field of view, (e) judging whether switching of fields of view is needed, (f) determining the position and temperature, (g) acquiring a reference temperature, (h) judging whether position compensation is needed, (i) switching to a small field of view, (j) determining focus bias quantity, (k) conducting forward compensation, and (l) conducting reverse compensation. The double-field of view thermal imager can be used for focus position compensation of the fields of view at different temperatures, is accurate, reliable, stable in operation, capable of meeting quick switching between the fields of view, and capable of being widely applied to many fields including weaponry, scout monitoring, people search and rescue and the like.