Rainfall intensity and soil and water conservation tillage measures have a significant impact on slope runoff, erosion sediment and soil trace elements. We studied the loss characteristics of Cu, Mo and Zn in tobacco planting red soil under different rain patterns, land preparation methods and cover conditions through field rain-fall observation methods. The results showed that:(1) Rainfall intensity had a significant effect on the loss of the three trace elements in the tobacco planting soil. With the increasing of rainfall intensity, the total loss of Cu, Mo and Zn followed the order of heavy rain>moderate rain>light rain. (2) Although straw covering and cross slope planting measures could effectively reduce erosion sediment caused by erosive rainfall, the enrichment ratio of Cu, Mo and Zn in sediment increased. (3) Compared with the treatment without straw mulch, Cu, Mo and Zn in runoff decreased by 44.99%, 47.42% and 62.24%, respectively, and the total loss of trace elements in sediment decreased by 67.35%, 56.88% and 67.85%, respectively, and straw mulching treatment had a significant effect on the reduction of total loss of trace elements (p<0.05). (4) Cu, Mo and Zn in the runoff of the cross slope planting treatment decreased by 43.31%, 46.39% and 45.62%, respectively, compared with the slope planting treatment. The three trace elements in the sediment decreased by 66.34%, 53.95% and 59.66%, respectively. The cross slope planting treatment significantly reduced the loss of the three trace elements (p<0.05). (5) The total loss of Cu, Mo and Zn in sediment was significantly higher than that in runoff, and the loss of Cu, Mo and Zn in runoff and sediment followed the order of Zn>Cu>Mo. This study results could provide theoretical basis and data support for effectively reducing and controlling the loss of trace elements caused by soil and water loss of typical tobacco planting red soil in southwest China and for soil and water conservation in tobacco planting red soil.