The escalating organic co-contamination in arable soils poses a severe threat to soil microecological health and sustainable agricultural development, presenting an urgent challenge to synergistically enhance cropland productivity and maintain microecological function. This review systematically summarizes the ubiquity, complexity, and microecological risks associated with organic co-contamination in cultivated lands, delving into the significant challenges and opportunities for reconstructing the health of cropland soil microbiomes under such stress. Given the limitations of traditional remediation methods, which are often insufficient and costly for complex co-contamination, a frontier strategy is needed. Emphasis is particularly placed on the application potential of modern molecular biology techniques, specifically Synthetic Microbiomes (SynMicro), in restoring the health of contaminated soil microbiomes. The review elucidates cutting-edge strategies for constructing functionally defined and structurally simplified synthetic microbial communities by integrating advanced techniques including metagenomics (to understand community structure and potential function), culturomics and high-throughput screening (to accelerate the isolation of functional microbial resources), genome-scale metabolic modeling (to enable rational design and prediction of microbial interactions), and Artificial Intelligence/Machine Learning (to facilitate intelligent design and optimization of SynMicro consortia). This work forecasts the promising prospects of SynMicro engineering in achieving synergistic multiple objectives critical for soil health reconstruction under co-contamination, such as enhanced pollutant reduction, effective soil-borne disease control, and improved soil fertility through optimized nutrient cycling. By highlighting the potential of SynMicro-based strategies empowered by these frontier technologies and outlining the current challenges, this review aims to provide novel theoretical insights and practical technical pathways for the reconstruction of cropland soil microecological health, ultimately contributing to ensuring national food security and promoting sustainable agricultural development.