The present work is focused on the fabrication of manganese dioxide/carbon dots (MnO₂/CDs) nanocomposites at room temperature in situ co-participation method in an aqueous medium and characterized. Our study showed that the concentration of CDs controls the morphology of MnO₂/CDs nanocomposite and also acted as a reducing agent to convert potassium permanganate (KMnO₄) to MnO₂. Subsequently, nanoflowers, quasi-spherical particles, broken, and interconnected chain type of morphology was observed by adding dispersion of 0.5, 1.0, 1.5, and 2.0 ml CDs in acetone to 1 mmol KMnO₄ aqueous solution in the corresponding MnO₂/CDs-0.5, MnO₂/CDs-1.0, MnO₂/CDs-1.5, and MnO₂/CDs-2.0 composites, respectively. A plausible mechanism on the transformation of morphology of MnO₂/CDs with CDs concentration is also provided. Further, the present work also focused for the first time on the application in the electromagnetic interference (EMI) shielding of MnO₂/CD nanocomposites due to the high dielectric and conductivity. Interestingly, MnO₂/CDs-2.0 (nanochains) exhibited the highest total EMI shielding efficiency (SET) of ~39.4 dB following reflection as dominant shielding mechanism due to the high aspect ratio, highest conductivity, high dielectric loss, and impendence mismatch.