Purpose: Obesity’s metabolic consequences are well documented; however, its neurobiological underpinnings remain elusive. This systematic review addresses a critical gap by synthesizing evidence on obesity-induced neuroplasticity across structural, functional, and molecular domains through advanced neuroimaging. Methods: According to PRISMA guidelines, we systematically searched (2015–2024) across PubMed/Web of Science, employing MeSH terms: (“Obesity” [Majr]) AND (“Neuroimaging” [Mesh] OR “Magnetic Resonance Imaging” [Mesh]). A total of 104 studies met the inclusion criteria. The inclusion criteria required the following: (1) multimodal imaging protocols (structural MRI/diffusion tensor imaging/resting-state functional magnetic resonance imaging (fMRI)/positron emission tomography (PET)); (2) pre-/post-intervention longitudinal design. Risk of bias was assessed via the Newcastle-Ottawa Scale. Key Findings: 1. Structural alterations: 7.2% mean gray matter reduction in prefrontal cortex (Cohen’s d = 0.81). White matter integrity decline (FA reduction β = −0.33, p < 0.001) across 12 major tracts. 2. Functional connectivity: Resting-state hyperactivity in mesolimbic pathways (fALFF + 23%, p-FDR < 0.05). Impaired fronto–striatal connectivity (r = −0.58 with BMI, 95% CI [−0.67, −0.49]). 3. Interventional reversibility: Bariatric surgery restored prefrontal activation (Δ = +18% vs. controls, p = 0.002). Neurostimulation (transcranial direct current stimulation (tDCS) enhanced cognitive control (post-treatment β = 0.42, p = 0.009). Conclusion: 1. Obesity induces multidomain neural reorganization beyond traditional reward circuits. 2. Neuroimaging biomarkers (e.g., striatal PET-dopamine binding potential) predict intervention outcomes (AUC = 0.79). 3. Precision neuromodulation requires tripartite integration of structural guidance, functional monitoring, and molecular profiling. Findings highlight neuroimaging’s pivotal role in developing stage-specific therapeutic strategies.