We construct a bipartite Euler system in the sense of Howard for Hilbert modular eigenforms of parallel weight two over totally real fields, generalizing works of Bertolini-Darmon, Longo, Nekovar, Pollack-Weston and others. The construction has direct applications to Iwasawa main conjectures. For instance, it implies in many cases one divisibility of the associated dihedral or anticyclotomic main conjecture, at the same time reducing the other divisibility to a certain nonvanishing criterion for the associated $p$-adic $L$-functions. It also has applications to cyclotomic main conjectures for Hilbert modular forms over CM fields via the technique of Skinner and Urban.