Neuropsychiatric disorders, such as schizophrenia, have a strong genetic basis and are linked to structural genomic changes such as copy number variations, including the 15q13.3 microdeletion. This study investigates the impact of the 15q13.3 microdeletion on neuronal maturation in the cerebral cortex, using a mouse model. We performed single-cell transcriptomics to analyse the transcriptomic changes in neuronal subtypes at different maturational stages. Compositional changes were validated with immunohistochemistry, while functional validation was conducted through calcium imaging and Patch-sequencing to identify alterations in neuronal function associated with the microdeletion. Our study revealed significant gene expression changes in adult 15q13.3/+ mice, particularly in a specialised subtype of somatostatin (Sst) neurons, Sst Chodl, also known as long-range Sst neurons. These alterations were absent during juvenile stages but expanded dramatically during late maturation, suggesting a critical role of late maturational processes in cortical dysfunction. Importantly, we identified Sst Chodl neurons as the subtype most affected by the microdeletion, demonstrating distinct functional perturbations compared to the rest of Sst neurons. While other Sst neurons show a decrease in calcium activity, Sst Chodl neurons reveal the opposite trend, hinting at distinct underlying processes. Additionally, by utilising patch-sequencing, we uncovered alterations in electrophysiological properties alongside potential gene targets implicated in shaping Sst Chodl behaviour. Our findings highlight the importance of considering neuronal diversity and maturation in understanding the mechanisms underlying neuropsychiatric disorders. We demonstrate that specific neuronal subtypes, particularly the Sst Chodl subtype, act as pivotal players in neuropsychiatric pathophysiology.