Observations of superconductivity and charge density waves (CDW) in graphene have been elusive thus far due to weak electron-phonon coupling (EPC) interactions. Here, we report a unique observation of anomalous transport and multiple charge ordering phases at high temperatures ( T 1 ∼ 213 K , T 2 ∼ 325 K ) in a 0D−2D van der Waals (vdW) heterostructure comprising of single layer graphene (SLG) and functionalized (amine) graphene quantum dots (GQD). The presence of functionalized GQD contributed to charge transfer with shifting of the Dirac point ∼ 0.05 eV above the Fermi level (ab initio simulations) and carrier density n ∼ − 0.3 × 10 12 cm − 2 confirming p-doping in SLG and two-fold increase in EPC interaction was achieved. Moreover, we elucidate the interplay between electron-electron and electron-phonon interactions to substantiate high temperature EPC driven charge ordering in the heterostructure through analyses of magnetotransport and weak anti-localization (WAL) framework. Our results provide impetus to investigate strongly correlated phenomena such as CDW and superconducting phase transitions in novel graphene based heterostructures.