Exploring the heterogeneity of carbon dots (C-Dots) is challenging because of the existence of complex structural diversity, and it is a demanding task for the development and designing of efficient C-Dots for various applications. Herein, we studied the role of the core state and surface state of C-Dots in heterogeneity via the successful investigation of the electron transfer (ET) process between different (blue, green, and red) emitting C-Dots and an electron acceptor methyl viologen (MV2+) using steady-state and time-resolved fluorescence and ultrafast transient absorption (TA) spectroscopic techniques. Selective excitation in the steady-state and time-resolved mode shows that the ET ability of the core state is higher than that of the surface state. Moreover, the kinetics of MV+˙ generation was probed using TA spectroscopy after the excitation of the core and surface state, where we observed that the surface state becomes less efficient due to the presence of an oxygen-containing functional group in the surface state, which acts as an electron scavenger. Moreover, the heterogeneity of the core and surface state was explored through the detection of the MV+˙ generation yield after the irradiation of UV and visible light (exciting the core and surface state). The result indicates that the graphitic nitrogen content in the core state and the oxygen-containing functional group in the surface state play an important role in the heterogeneity in the structure and the ET process. Our findings on the fundamental understanding of the heterogeneity of different emissive C-Dots will provide a new way of designing and developing a metal-free light-harvesting system.