We consider two-phase flow in a heterogeneous porous medium with highly permeable fractures and low permeable periodic blocks. The flow in the blocks is assumed to be in local capillary disequilibrium and described by Barenblatt’s relaxation relationships for the relative permeability and capillary pressure. It is shown that the homogenization of such equations leads to a new macroscopic model that includes two kinds of long-memory effects: the mass transfer between the blocks and fractures and the memory caused by the microscopic Barenblatt disequilibrium. We have obtained a general relationship for the double nonequilibrium capillary pressure which represents great interest for applications. Due to the nonlinear coupling and the nonlocality in time, the macroscopic model remains incompletely homogenized in general case. The completely homogenized model was obtained for two different regimes. The first case corresponds to a linearized flow in the blocks. In the second case, we assume a low contrast in the block-fracture permeability. Numerical results for the two-dimensional problem are presented for two test cases to demonstrate the effectiveness of the methodology.