Na3V2(PO4)3 is one of the most important cathode materials for sodium-ion batteries, delivering about two Na extraction/insertion from/into the unit structure. To understand the mechanism of sodium storage, a detailed structure of rhombohedral Na3V2(PO4)3 and its sodium extracted phase of NaV2(PO4)3 are investigated at the atomic scale using a variety of advanced techniques. It is found that two different Na sites (6b, M1 and 18e, M2) with different coordination environments co-exist in Na3V2(PO4)3, whereas only one Na site (6b, M1) exists in NaV2(PO4)3. When Na is extracted from Na3V2(PO4)3 to form NaV2(PO4)3, Na+ occupying the M2 site (CN = 8) is extracted and the rest of the Na remains at M1 site (CN = 6). In addition, the Na atoms are not randomly distributed, possibly with an ordered arrangement in M2 sites locally for Na3V2(PO4)3. Na+ ions at the M1 sites in Na3V2(PO4)3 tend to remain immobilized, suggesting a direct M2-to-M2 conduction pathway. Only Na occupying the M2 sites can be extracted, suggesting about two Na atoms able to be extracted from the Na3V2(PO4)3 structure.