The invention relates to a relief well and accident well connection detection system and a detection method thereof. The detection system comprises a three-component magnetic core probe and a transmission unit and the like. The three-component magnetic core probe consists of a Z probe, an X probe, and a Y probe, wherein each two of the Z probe, the X probe, and the Y probe are perpendicular to each other; and the X probe, the Y probe and the Z probe include transmitting coils and receiving coils respectively. The transmitting unit is used for transmitting a transient excitation signal; the transmitting coils of the Z probe, the X probe, and the Y probe receive transient excitation signals and spread the transient excitation signals to an accident well by a relief well to generate a Z-direction induction signal, an X-direction induction signal, and a Y-direction induction signal; the receiving coils of the Z probe, the X probe, and the Y probe receive the Z-direction induction signal, the X-direction induction signal, and the Y-direction induction signal correspondingly and respectively; the received Z-direction induction signal, X-direction induction signal, and Y-direction induction signal are transmitted to a ground unit by a receiving unit and a collection and transmission unit; and the ground unit calculates a distances between the accident well and the three-component magnetic core probe and directions of the accident well and the three-component magnetic core probe according to the Z-direction induction signal, the X-direction induction signal, and the Y-direction induction signal and then the information is displayed.