The invention provides a capturing method of Beidou second-generation B1 signals and a system thereof. The capturing method comprises steps of 1: changing processed a B1 signal received by an antenna into a digital intermediate frequency signal; 2: receiving the digital intermediate frequency signal, peeling carrier waves, extracting and then storing data; 2: interpolating the data; 3: searching the data and peeling the carrier waves; 4: performing DFT for the data on 4 points; 5: peeling carrier waves for the data, performing FFT, then performing IFFT, obtaining related peak results, and then processing all data so as to related peak results; and 6: sequencing the related peak results, wherein if the biggest peak value is larger than a captured threshold, it shows that the B1 signal has been captured, and otherwise, the B1 signal has not been captured. The invention also provides a capturing system of the Beidou second-generation B1 signals. According to the invention, 4ms coherent integration of the B1 signals can be achieved, capturing sensitivity of the B1 signals is increased and balance between computation amount and capturing sensitivity can be obtained.