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As a non-renewable strategic resource, trace helium (He < 0.1%) is critical for sustainable industrialization and innovation. However, its precise assessment in natural gas reservoirs presents significant challenges due to its extremely small kinetic diameter (0.26 nm) and high diffusivity, which lead to severe escape risks and detection uncertainty. To quantify systematic errors introduced by sampling containers and elucidate the underlying physical mechanisms, this study established a rigorous comparative framework to evaluate the immediate capture efficiency and long-term stability (30 days) of trace helium in double-valve stainless steel cylinders versus aluminum-plastic composite bags (total n = 24). Results demonstrate fundamental disparities in the barrier mechanisms and mass transfer characteristics of the two containers. Immediate analysis reveals that composite bags, limited by a low-pressure laminar purging mode, fail to eliminate residual air within the dead volume. This results in a marked background dilution effect and anomalous initial O2 concentrations. Long-term monitoring indicates that trace helium in composite bags follows the polymeric “solution-diffusion” mechanism, exhibiting severe non-linear decay (up to 78.7% loss over 30 days) accompanied by bi-directional permeation and irreversible component exchange with atmospheric air. In contrast, stainless steel cylinders effectively block physical permeation pathways due to their dense face-centered cubic (FCC) lattice and metal-to-metal sealing structure. Observed data fluctuations (Δ < 0.008 mol%) fall entirely within the reproducibility limits defined by gas analysis standards, confirming a metrologically zero-loss characteristic. Error analysis further reveals that systematic bias introduced by bag permeability (~ 79%) exceeds random instrumental error (< 2%) by a factor of approximately 40, establishing storage container integrity as the decisive limiting factor for detection accuracy. Consequently, the applicability boundary for flexible bags is strictly confined to immediate, on-site rapid screening (< 24 h) under mild environmental conditions. We recommend establishing a hierarchical container selection protocol based on “component characteristics, storage duration, and logistical operational windows.” Furthermore, current sampling guidelines should be revised to mandate the use of high-pressure metal-sealed cylinders for any medium-to-long-term archiving of trace noble gases. Ensuring geological data fidelity through such stringent metrological controls is essential to prevent resource misallocation, thereby promoting responsible exploration and production practices.