Browning is the primary physiological damage that shortens the postharvest life and deteriorates the quality of stored fruits. Controlled atmosphere (CA) storage has been shown to be effective in alleviating the browning of ‘Xifu 1′ in-hull walnut; however, its alleviation mechanism is less understood. To further explore the effect and regulatory mechanism of CA on the browning of fresh in-hull walnut, we stored four varieties of in-hull walnuts under CA-treated (5% O2 + 7.5% CO2) and untreated conditions at 0 ± 0.5 °C with 70–80% relative humidity for 70 d. The indicators related to browning and γ-aminobutyric acid (GABA) metabolism were measured until 56 d of storage. The results showed that the CA significantly increased GABA levels by maintaining higher activities of glutamate decarboxylase (GAD), GABA transaminase (GABAT) and succinate dehydrogenase (SDH). This reduced the changes in the browning index (BI), color values, and respiration rate (RR) of the four walnut fruit varieties compared with controls during storage. Consistent with the active GABA metabolism, higher energy charge (EC) and adenosine triphosphate (ATP), succinic acid (SA), malic acid (MLA), fumaric acid (FA), and citric acid (CTA) contents were also observed in the CA-treated walnut hull compared to the controls. The epicarp degradation of the CA-treated ‘Xifu 1′ walnut fruit occurred later, and their mitochondria and cells maintained better integrity compared to the controls. Among the differentially expressed genes (DEGs) screened via RNA-Sequencing (RNA-Seq), 32 were annotated as part of the citrate cycle (TCA cycle) pathway, and 27 were annotated in the GABA metabolism pathway. Real-time quantitative PCR (RT-qPCR) analysis showed that eight candidate genes were closely related to the effect of CA on the synthesis, transport, and transformation of GABA. In conclusion, CA effectively controlled the browning of different varieties of fresh in-hull walnuts by enhancing GABA metabolism and maintaining energy balance.