Vitrimers are a class of polymers that flow when heated but are insoluble. Vitrimers are made of covalent networks with dynamic links and/or cross-links that undergo an associative exchange reaction. These dynamic cross-links enable vitrimers to have interesting mechanical/rheological behavior, self-healing, adhesive, and shape memory properties. We demonstrate that vitrimers can self-assemble into complex meso- and nanostructures when cross-links and backbone monomers strongly interact. Vitrimers featuring polyethylene (PE) as the backbone and dioxaborolane maleimide as the cross-linkable moiety were studied in both the molten and semicrystalline states. We observed that PE vitrimers macroscopically phase separated into dioxaborolane maleimide-rich and -poor regions and characterized the extent of phase separation by optical transmission measurements. This phase separation can explain the relatively low insoluble fractions and overall crystallinities of PE vitrimers. Using synchrotron-sourced small-angle X-ray scattering (SAXS), we discovered that PE vitrimers and their linear precursors microphase separated into hierarchical nanostructures. Fitting of the SAXS patterns to a scattering model strongly suggests that the nanostructures-which persist in both the melt and amorphous fraction of the semicrystalline state-may be described as dioxaborolane maleimide-rich aggregates packed in a mass fractal arrangement. These findings of hierarchical meso- and nanostructures point out that incompatibility effects between network components and resulting self-assembly must be considered for understanding behavior and the rational design of vitrimer materials.