Typical ~10-kilobase tandem duplications associated with Brca1-deficient tumors were revealed by analysis of human cancer genome sequences, but the present underlying mechanisms remain defective. Here, we show two-ended and one-ended DNA strand breaks (DSBs) induced TDs mediated by first round of equal strand invasion and second round of unequal strand invasion mediated by MH are stimulated due to aberrant termination in Brca1-deficient cells with repeat-independent TD reporter. Furthermore, we provide a first indication that breakpoint is not junction of TD due to two round of strand invasion. We developed a new strategy using PCR-amplified with inverted primer to define the mechanisms underlying Brca1-associated TDs. BRCA1 is required for maintaining genome stability by suppression of TDs mediated by two round of strand invasion and MH-mediated one round of strand invasion, moreover, suppresses one-ended DSBs converted from Cas9n-induced nicks by DNA replication induced TDs mediated by non-homologous end joining (NHEJ) or microhomologous mediated end joining (MMEJ) termination. At last, we demonstrated that Rad51 loading is dispensable for BRCA1-mediated TD suppression with deletion of CC domain of Brca1. These results provide a new insight of mechanisms for Brca1-linked TDs and for the design of new genetic/biological based strategies to clinical treatment.