To answer the challenges of using nitrilotriacetic acid (NTAA) as an efficient, recyclable, and durable acidic nanocatalyst, a novel, versatile, engineerable, affordable, eco‐friendly acidic heterogeneous magnetic nanocatalyst has been synthesized with high thermal stability and excellent catalytic efficiency through immobilization of NTTA on the surface of the functionalized magnetite core‐shell. Fe3O4@SiO2‐NH‐NTAA, has been synthesized and presented here. This nanomagnetic catalyst, Fe3O4@SiO2‐NH‐NTAA, was fully identified and characterized through analytical techniques such as FTIR, FESEM, TEM, EDX, elemental mapping, TGA‐DSC, DLS, VSM, and XRD, in addition to theoretical calculations based on DFT/B3LYP/6‐311++G(d, p). Its catalytic capability as well as easy separation, recoverability, and reuseability were examined in the one‐pot preparation of pyrimido[4,5]quinolone‐2,4‐diones under mild conditions, where the high performance of the Fe3O4@SiO2‐NH‐NTAA magnetic nano‐catalyst was proved by excellent reaction yield (>98 %) and the catalyst's recovery efficiency (>98 %). Due to the presence of NTAA's zwitterionic forms in the outermost layer of Fe3O4@SiO2‐NH‐NTAA, this acidic catalyst causes the progress and control of the three‐component reaction in this article well and in the desired direction.