Individuals rely on various frames of reference (FORs), such as an egocentric FOR (EFOR) and intrinsic FOR (IFOR), to represent spatial information. Previous behavioral studies have shown different IFOR-IFOR (II) and EFOR-IFOR (EI) conflict effects and an effect of their interaction. However, the neural mechanism of conflict processing between two FOR-based conflicts is unclear. In the current ERP study, two FOR-based conflicts were manipulated using a two-cannon task to elucidate common and distinct brain mechanisms that underlie FOR-based conflict processing. The behavioral results showed that both conflicts exhibited longer reaction times and larger error rates in the II (180 degrees cannon angle) and EI (target cannon pointed down) incongruent conditions than in the II (0 degrees cannon angle) and EI (target cannon pointed up) congruent conditions and that an interaction existed between the two conflicts. The ERP results indicated that, for both conflicts, more negative N2 amplitudes and less positive P3 amplitudes occurred in the incongruent conditions than in the congruent conditions, and the interactions between the two conflicts during later P3 amplitudes were significant. Time-frequency analysis further indicated that, in the early time window, the II conflict and the EI conflict specifically modulated power in the theta bands and beta bands, respectively. In contrast, in the later time window, both conflicts modulated power in the alpha and beta bands. In summary, our findings provide insights into the potential existence of two specific early conflict monitoring systems and a general late executive control system for FOR-based conflicts.