In order to select cover crop varieties suitable for the thin layer black soil region and possessing the ability to mitigate soil compaction of the deeper soil layers, an experiment was conducted in the typical black soil area in Jilin Province, uncompacted and compacted treatments were established, and different cover crop varieties were planted in spring and autumn periods, including alfalfa, hairy vetch, sweet clover, erect milkvetch, sesbania, sorghum hybrid sudangrass, radish, rapeseed, chicory, silphium perfoliatum, rumex, ryegrass, a mixture of sesbania+sorghum hybrid sudangrass+radish+chicory (mixed planting 1), and a mixture of sweet clover+ryegrass+ rapeseed+rumex (mixed planting 2). The responses of cover crop root systems to compacted soil were analyzed. The results showed that mechanical compaction treatment in spring significantly increased soil bulk density in the 0-50 cm soil layer. Three months later, compacted treatment still showed significantly higher soil bulk density in the 10-50 cm soil depth and greater penetration resistance in the 0-30 cm soil depth than the uncompacted treatment. Root dry weight proportions and root dry weight densities of various cover crops in different soil depths were significantly influenced by compaction. In the spring planting cover crops, in the 30-50 cm compacted soil layer, alfalfa exhibited the highest proportion of root dry weight, while sorghum hybrid sudangrass, sesbania, and mixed planting 2 demonstrated greater root dry weight density. In the autumn planting cover crops, ryegrass had the highest proportion of root dry weight, and rapeseed, chicory, and mixed planting 1 exhibited higher root dry weight density. Based on root dry weight proportion ratio (Ratio1) and root dry weight density ratio (Ratio2) proposed in this study as the parameters for assessing the penetration capability of roots in the 30-50 cm compacted soil layer, cover crop species with relatively low susceptibility to compaction and strong penetration ability in compacted soil (30-50 cm) were selected: sorghum hybrid sudangrass, sesbania and alfalfa for spring planting, while rapeseed, mixed planting 1 and ryegrass for autumn planting.