Light harvesting by LH1 and LH2 antenna proteins in the photosynthetic membranes of purple bacteria has been extensively studied in recent years for the fundamental understanding of the energy transfer dynamics and mechanism. Here we report the inhomogeneous structural organization of the LH2 complexes in photosynthetic membranes, giving evidence for the existence of energetically coupled linear LH2 aggregates in the native photosynthetic membranes of purple bacteria. Focusing on systematic model analyses, we combined AFM imaging and spectroscopic analysis with energetic coupling model analysis to characterize the inhomogeneous linear aggregation of LH2. Our AFM imaging results reveal that the LH2 complexes form linear aggregates with the monomer number varying from one to eight and each monomer tilted along the aggregated structure in photosynthetic membranes. The spectroscopic results support the attribution of aggregated LH2 complexes in the photosynthetic membranes, and the model calculation values for the absorption, emission and lifetime are consistent with the experimentally determined spectroscopic values, further proving a molecular-level understanding of the energetic coupling and energy transfer among the LH2 complexes in the photosynthetic membranes.