Microscopic structures and magnetic properties are investigated for Fe5-xGeTe2 single crystal, recently discovered as a promising van der Waals (vdW) ferromagnet. An Fe atom (Fe(1)) located in the outermost Fe5Ge sublayer has two possible split-sites which are either above or below the Ge atom. Scanning tunneling microscopy shows root 3 x root 3 superstructures which are attributed to the ordering of Fe(1) layer. The root 3 x root 3 superstructures have two different phases due to the symmetry of Fe(1) ordering. Intriguingly, the observed root 3 x root 3 ordering breaks the inversion symmetry of crystal, resulting in substantial antisymmetric exchange interaction. The temperature dependence of magnetization reveals a sharp magnetic anomaly suggesting helical magnetism of the Fe5-xGeTe2 due to its non-centrosymmetricity. Analytical study also supports that the observed ordering can give rise to the helimagnetism. The work will provide essential information to understand the complex magnetic properties and the origin of the new vdW ferromagnet, Fe5-xGeTe2 for future topology-based spin devices.