We studied the co-assembly of an oppositely changed binary mixture of selenium-doped carbon quantum dots (Se-CQDs) and N,N-dimethyl octylamide-propyl tertiary amine (DOAPA) through turbidity, ζ potential measurement, and cryogenic transmission electron microscopy (cryo-TEM) with the aim of fabricating supramolecular assemblies with multiple dimensions and novel morphologies. The Se-CQD/DOAPA binary mixture exhibited abundant phase behavior, in which an isotropic phase (I1) was first observed, followed by turbidity (T), precipitation (P), and a second isotropic phase (I2), as the DOAPA concentration increased. Then we focused on investigating the morphologies of samples. In cryo-TEM observations, spherical aggregates were observed in all phase sequences, whereas the aggregates have different ζ potentials and sizes. In the I2 phase, interesting nanocapsule-like aggregates and spindle-like aggregates can be identified in addition to spherical aggregates. In combination with the rheological behaviors of the I2 phase solution and the detailed structure of the aggregates from enlarged cryo-TEM images, it is possible that the Se-CQDs and DOAPA co-assemble with novel network-like building blocks. The turbid solutions were found to be responsive to pH in phase P, and spherical aggregates were obtained at pH 6.5 but turned into vesicles when the pH reached 5.0. On the basis of these findings, CQDs and surfactants can be good structural building blocks for supramolecular structures, and the diverse morphologies of aggregates offer the prospect of multiple applications in the future.