Shallow natural gas has considerably impacted tunnel engineering in the southwestern Sichuan region in China. To address this issue, based on geological analysis and engineering geological exploration, the distribution characteristics and factors controlling the shallow natural gas are analyzed via sealing gas accumulation tests and layered detection tests. The engineering effects and countermeasures of shallow natural gas enrichment on tunnel construction are analyzed. Results reveal that deep natural gas tends to migrate to the shallow surface via faults, joints, and fissures, forming a rich group with higher natural gas concentration in the Quaternary special reservoir caprock combination with clay as the caprock layer and pebble layer as the reservoir. The high, low, and slight gas concentration areas of the Chengdu-Meishan line tunnel are located in the pebble layer, strongly weathered mudstone and some pebble layers, and intact mudstone and thin pebble layer of the overlying clay layer. Moreover, shallow natural gas impacts construction safety, cost, and duration of tunnel engineering and poses a major challenge during engineering survey. To address this issue, tunnel design and plans must be optimized and prevention and control measures must be undertaken. Additionally, operation and maintenance plans must be devised in areas containing shallow natural gas.