Purpose <p>Stabilization of loess microstructure is essential for soil and water management, plant roots can improve soil aggregate structure, which is easily dispersed and destroyed during wetting and drying alternation. This study tried to quantify the effects of plant roots on loess soil aggregates under wetting and drying alternation.</p> Methods <p>Remolded loess (loam and sandy loam) columns with and without growing alfalfa (<i>Medicago sativa</i> L.) were controlled at a soil bulk density of 1.2&#xa0;g·cm^− 3 and kept indoor cultivation for 28 days. Root investigation and soil aggregate analysis were conducted on the columns under five treatments of wetting and drying alternation (0, 1, 2, 3, and 4 cycles).</p> Results <p>Wetting and drying alternation slowed alfalfa root growth, linearly reducing root morphology indexes with cycles increased. This process simultaneously disrupted soil aggregation, significantly decreasing aggregate size in non-rooted soil. However, alfalfa roots were effective in improving soil aggregate under these wetting and drying conditions. The mean weight diameter, geometric mean diameter, and water-stable aggregates content of loess &gt; 0.25&#xa0;mm were 2.33, 1.72, and 2.58 times higher in the rooted loam, and 3.12, 2.88, and 3.0 times higher in the rooted sandy loam than those in the corresponding non-rooted soil after four cycles of wetting and drying alternation.</p> Conclusions <p>Plant roots could significantly relieve the destructive effect of wetting and drying alternation on soil aggregates. The protective effect of the roots on soil aggregate by the roots was greater in the sandy loam than in the loam.</p>