In this work, we have designed and developed a novel surface plasmon resonance (SPR) aptasensor based on the two-dimensional (2D) Zr-doped MnB4 nanosheets decorated with Au nanoparticles (NPs) (denoted as AuNPs@Zr/MnB4) for efficiently detecting nucleolin (NCL).The established AuNPs@Zr/MnB4 dual-interface Schottky heterojunction benefitted from the modulatory effect of the density state of Mn sites in MnB4 through Zr doping and the incorporation of Au NPs, endowing it with high optical absorption efficiency, fast charge carrier mobility, and improved work function. Thus, it exhibited enhanced interface electric field energy of the surface plasmon effect, amplifying SPR response. Moreover, the rich Zr sites in AuNPs@Zr/MnB4 considerably promoted the immobilization of large amounts of AS1411 aptamer strands through the Zr–O–P covalent bond, coordination effect, and van der Waal force, rendering the high detection sensitivity to NCL. The AuNPs@Zr/MnB4-based SPR aptasensor demonstrated a wide dynamic range (1.0 ag mL−1 to 100 ng mL−1) and an ultralow detection limit (0.44 ag mL−1). This work introduced a new strategy for the construction of SPR aptasensors to enable the sensitive inspection of biomarkers and extended the application of 2D MBene nanomaterials in biosensing and biological diagnosis.