We show that when two toric Calabi-Yau 3-folds and their corresponding toric varieties are related by a birational transformation, they are associated with a pair of dimer models on the 2-torus that define dimer integrable systems, which themselves become birationally equivalent. These integrable systems defined by dimer models were first introduced by Goncharov and Kenyon. We illustrate this equivalence explicitly using a pair of dimer integrable systems corresponding to the abelian orbifolds of the form C^3/Z_4 x Z_2 with orbifold action (1,0,3)(0,1,1) and C/Z_2 x Z_2 with action (1,0,0,1)(0,1,1,0), whose spectral curves and Hamiltonians are shown to be related by a birational transformation.