Foundation treatment piles are crucial for enhancing the bearing capacity and stability of weak foundations and are widely utilized in construction projects. However, owing to the complexity of geological conditions, traditional construction methods fail to meet the demand for low-carbon development. To address these challenges, this study introduced a comprehensive decision-making approach that considers the impact of stratum variability on greenhouse gas (GHG) emissions and pile bearing capacity from the design phase. During the design process, the GHG emissions and bearing capacities of deep cement mixing (DCM) and high-pressure jet grouting (HPJG) piles were quantitatively assessed by analyzing the environmental and performance impacts of foundation treatment piles related to materials, transportation, and equipment usage. The results suggest that the bearing capacity of piles in shallow strata is highly susceptible to stratum variability. Using piles with a diameter of 800 mm and a length of 20 m as an example, compared with DCM piles, HPJG piles demonstrated a superior bearing capacity; however, their total GHG emissions were 6.58% higher, primarily because of the extensive use of machinery during HPJG pile construction. The GHG emissions of foundation treatment piles in shallow strata were influenced more by geological variability than those in deep strata. Sensitivity analysis revealed that the pile diameter is a critical determinant of GHG emissions and bearing capacity. Based on the bearing capacity–GHG emission optimization framework, a foundation treatment strategy that integrates overlapping and spaced pile arrangements was introduced. This innovative construction method reduced the total GHG emissions by 22.7% compared with conventional methods. These research findings contribute to low-carbon design in the construction industry.