Background/Objectives: This study explores the micro-structure of celiac ganglia using two-photon microscopy (TPM) to highlight histological features in neurodegenerative conditions. Neurodegenerative diseases like Parkinson’s disease (PD) are linked to dysautonomia, impacting autonomic regulation and leading to significant gastrointestinal and autonomic symptoms. Our research compares imaging results from TPM and SHG microscopy, visualizing neuronal integrity, collagen distribution, and the architectural organization of celiac ganglia. SHG specifically allows detailed imaging of collagen fibers and neuronal structures, revealing alterations in collagen density and organization that correlate with dysautonomia. Methods: The cross-sectional study was conducted at “Dr. Carol Davila” Central Military Emergency University Hospital, Bucharest, Romania, involving 70 participants diagnosed with PD (Hoehn and Yahr stages 2–4), including 35 with dysautonomia and 35 without. We utilized samples from PD patients with and without dysautonomia, applying immunohistochemical markers for sympathetic neurons. Results: Our findings reveal significant pathological changes in neuronal structure and collagen architecture. Immunohistochemical markers (neuropeptide Y, neurofilament heavy chain (NF-H), and tyrosine hydroxylase) were employed to characterize sympathetic neurons, while TPM and SHG provided high-resolution imaging of neuronal integrity and extracellular matrix composition. Conclusions: These imaging techniques present a promising tool for early diagnosis and assessment of neurodegeneration and dysautonomia in PD patients. Moreover, these techniques may represent a critical bridge between histopathological findings and clinical manifestations, underscoring their role in enhancing our understanding of neurodegeneration and autonomic dysfunction in Parkinson’s disease.