The invention provides a three-dimensional location positioning system and method based on beacons and positioning network elements. The three-dimensional location positioning system comprises ID transmitting beacons, positioning network elements and a cloud server; the ID transmitting beacons periodically send own ID information; after the positioning network elements receive the ID information of the ID transmitting beacons, the positioning network elements package the ID information, the longitude and latitude information of the positioning network elements and network element environment information and transmit to the cloud server; the cloud server obtains the geographical location information of each ID transmitting beacon and the positioning network elements through the received information and stores the geographical location information. According to the system and the method provided by the invention, the mode that the traditional positioner exclusively uses a data channel is broken; comprehensive transmission fusion of the positioning network element layer is realized; the data connection paths of the positioning network elements are enhanced; and the anti-shielding capability of the three-dimensional location positioning system is improved.