We consider M-theory compactification on a compact elliptic Calabi-Yau 3-fold, where the BPS partition function counts the degeneracies of 5D BPS particles associated with M2-branes on holomorphic 2-cycles. These BPS particles carry spins (j_L, j_R) under the 5D rotation symmetry in the spatial directions. In our work, we propose a refined BPS counting for compact elliptic Calabi-Yau 3-folds using Wilson line expectation values in the 5D gauge theories engineered from the local limits of the compact Calabi-Yau 3-folds.