The invention provides a double-frequency ionosphere measuring method based on a China area positioning system and a system thereof. The method comprises the steps of performing upconversion of a linear frequency modulating signal to a double-frequency FM signal, through transmitting out by an antenna, performing forwarding by a satellite transponder for forming a first echo signal and a second echo signal; after the first echo signal and the second echo signal are received by the antenna, performing down-conversion through a receiving channel for obtaining a fixed intermediate frequency signal, and performing signal acquisition; feeding a double-frequency RF signal into a receiving channel through an inner scaling extension set, thereby acquiring a first inner scaling signal and a secondinner scaling signal; acquiring the propagation time delay of a first-path signal according to the first echo signal and the first inner scaling signal which are synchronously acquired, and acquiringa propagation time delay of a second-path signal similarly; and calculating an ionosphere TEC according to the relationship among the propagation time delay of the first-path signal, the propagation time delay of the second-path signal and the ionosphere TEC. According to the method, a mathematical model between the space propagation time delay difference of double frequency signals and the ionosphere TEC is established, and accurate measurement for the ionosphere TEC is realized.