The present numerical study provides a detailed topology-based understanding of the three-dimensional vortical flow interaction process for an elevated square cross jet of low-to-moderate velocity ratio (0.25 ≤R≤ 4.0). For R≤ 0.5, a steady inner-vortex (Iv) formed in the jet pipe owing to the leading-edge jet shear layer roll up as a spiral node. The kinematics of the limiting streamlines and separation-attachment patterns along the jet shear layer confirm the presence of the Iv. For 0.5 < R≤ 1.2, the Iv partly escapes, as its front side remains attached to the pipe hole and the azimuthally extended lee side moved out in a tilted fashion. Moreover, the continuous vortex shedding from the stack created a dominant von Karman-like street that grew along the lower side of the jet wake. Distinctly for R = 4, the intruded convective crossflow pulled up the spiral front node/Iv out of the pipe, which also shifted the onset of the Kelvin–Helmholtz instability upward. Significantly, the pulled-up node/Iv facilitated the above-orifice anti-kidney vortical evolution of the issuing jet shear layer. For the first time, the study displays the triple-deck growth of the kidney and anti-kidney vortices above an elevated square cross jet for 2.5 ≤ R ≤ 4.0 and 1000 ≤ Re ≤ 2000. For 0.5 ≤ R ≤ 1.2, the double-decked kidney vortices involving the primary and the secondary pairs grew above the central jet column. However, the stronger primary pair fast entrained the secondary one close to the orifice edge. With R ≥ 2.5, the lateral jet shear layer experienced an unexpected windward concave warping and restructured to evolve as the anti-kidney third-deck situated above the mid-deck primary kidney vortices. The topological shear layer folding and created kidney/anti-kidney vortices above the elevated square cross jet, for 0.25 ≤R≤ 4.0, appear consistent with the past measurements for a high aspect ratio elliptic flush jet. The anti-kidney vortical growth though was not detected above a square flush jet. The dominating above-orifice topological node in the high-pressure area ensured the anti-kidney vortical growth via the generated local pressure-gradient induced flow acceleration.