The invention discloses an indoor positioning system and method based on ultrasonic waves. The system comprises an ultrasonic wave transmitting unit, an ultrasonic wave receiving unit and a data processing unit, wherein the ultrasonic wave transmitting unit, the ultrasonic wave receiving unit and the data processing unit are sequentially connected. The indoor positioning method implemented by the system includes the steps that the ultrasonic wave transmitting unit generates the two kinds of ultrasonic waves different in frequency and transmits the ultrasonic waves according to a preset sequence at a preset time interval; the ultrasonic wave receiving unit receives the ultrasonic waves sent out by the ultrasonic wave transmitting unit, filters out interference clutters and transmits processed signals to the data processing unit; the data processing unit processes data transmitted in by the ultrasonic wave receiving unit to obtain three-dimensional coordinates of a moving object. Due to the special design of the ultrasonic wave receiving unit and the application of time difference, the time synchronization problem of the ultrasonic wave transmitting end and the ultrasonic wave receiving end is solved, and the moving object can be positioned only by means of receiving the signals without transmitting the signals; positioning and calculating are efficient, and the moving object can be positioned accurately in space.