We construct the JSJ tree of cylinders T c for finitely presented, one-ended, two-dimensional right-angled Coxeter groups (RACGs) splitting over two-ended subgroups in terms of the defining graph of the group, generalizing the visual construction by Dani and Thomas [DT17] given for hyperbolic RACGs. Additionally, we prove that T c has two-ended edge stabilizers if and only if the defining graph does not contain a certain subdivided K 4 . By use of the structure invariant of T c introduced by Cashen and Martin [CM17], we obtain a quasi-isometry-invariant of these RACGs, essentially determined by the defining graph. Furthermore, we refine the structure invariant to make it a complete quasi-isometry-invariant in case the JSJ decomposition of the RACG does not have any rigid vertices.