The key factors governing the single-phase or multi-phase structural change behaviors during the intercalation/deintercalation of guest ions have not been well studied and understood yet. Through systematic studies of orthorhombic Fe2(MoO4)3 electrode, two distinct guest ion occupation paths, namely discrete one for Li and pseudo-continuous one for Na, as well as their relationship with single-phase and two-phase modes for Na(+) and Li(+), respectively during the intercalation/deintercalation process have been demonstrated. For the first time, the direct atomic-scale observation of biphasic domains (discrete occupation) in partially lithiated Fe2(MoO4)3 and the one by one Na occupation (pseudo-continuous occupation) at 8d sites in partially sodiated Fe2(MoO4)3 are obtained during the discharge processes of Li/Fe2(MoO4)3 and Na/Fe2(MoO4)3 cells respectively. Our combined experimental and theoretical studies bring the new insights for the research and development of intercalation compounds as electrode materials for secondary batteries.