Soil salinization is the accumulation of soluble salts in the soil, particularly in the root zone. The excess salt has severely constrained the agricultural productivity and the carbon sequestration capacity of the ecosystems in arid regions. Subsurface pipe drainage (SPD) technology can be expected to serve as an effective engineering measure to ameliorate the saline-alkali soils. It is often needed for its environmental sustainability in climate change mitigation. In this study, a systematic assessment was performed on its net environmental impact, specifically, the trade-off between its life-cycle carbon costs and the ecosystem carbon benefits. A field experiment was conducted in the Yanqi Basin of Xinjiang, from the representative arid inland area under severe secondary salinization. The carbon balance of the SPD system was quantified to clarify the synergistic water-salt regulation with the soil-crop-carbon sequestration. Four treatments were set: a control group (CK) under conventional flood irrigation and three SPD systems with the varying parameters (T1: burial depth 1.4 m, spacing 20 m; T2: depth 1.6 m, spacing 20 m; and T3: depth 1.6 m, spacing 40 m). Seasonal dynamics of the soil salinity were measured to evaluate the sunflower (Helianthus annuus L.) yield at harvest. The carbon sink of the vegetation was quantified after measurement. Crucially, a carbon accounting framework was applied to the full life cycle. The direct carbon costs were systematically integrated with the indirect carbon net in the ecosystem, including the emissions from the material production, on-site construction activities, and operation. The results demonstrated that all SPD treatments significantly reduced the rootzone (0-60 cm) soil salinity, compared with the CK. The high efficacy of the SPD was achieved to effectively break the salt stress on the crops. The rhizosphere environment directly improved the agricultural productivity. The underground pipeline treatment has significantly increased the yield of oil sunflowers. Consequently, the biomass production shared the major increase in the vegetation carbon sink, compared with the CK. Statistical analysis confirmed that a strong "desalination-yield increase-carbon sequestration" chain shared the significant negative correlations between soil salinity and both yield and carbon sink. The T1 treatment (1.4 m depth, and 20 m spacing) was consistently achieved in the best ecological-economic balance, indicating the effective desalination with the superior carbon efficiency among the tested designs. The carbon accounting revealed that the vegetation carbon sink increment of 10113 to 10421 kg/hm² was overwhelmingly offset in a strongly positive net carbon balance, while the SPD system incurred the direct carbon costs from 5310 to 5820 kg/hm². This finding can provide robust evidence to strategically design the SPD technology and synergistically enhance both the productive capacity and the ecological function, particularly the carbon sequestration potential of the saline-alkali lands. The vital technical parameters can be integrated into the scalable saline land remediation for the regional and national carbon neutrality.