A split-plot field experiment was conducted in farmers’ paddy fields in 2014 to study the effects of direct seeding (DS) and mechanical transplanting (MT) on root traits of indica hybrid rice with a new rice root sampler. The main results were as follows: 1) With the new rice root sampler, sampling and stratified sampling could be conducted accurately and conveniently; 2) Total root length, root volume and the number of root tips before transplanting and after recovery under MT and artificial transplanting (AT) were all less than those under DS, while the root growth rate and root-shoot ratio under MT and AT were higher than those under DS in the recovery date; 3) Root system under DS grew rapidly in the early growth stage with a larger root number and a thinner root type, and the number of root tips and root-shoot ratio were larger than those under MT and AT in the heading stage; Having the advantage of backwardness, the root system under MT grew rapidly after the active tillering stage, and the total root length and root volume were the largest in the heading stage; while root under MT was thicker with a smaller number and the least root-shoot ratio. 4) Root under DS and MT distributed shallowly compared with AT, root dry weight in 0-10 cm soil layer under DS, MT and AT accounted for 76.9%, 76.5% and 76.5%, respectively, and the proportion of root dry weight in 10-20cm soil layer and deeper than 20 cm soil layer under DS and MT were less than AT; while horizontally, the root dry weight of rice under DS accounted for 3.5% and 3.3% higher than under MT and AT, respectively within 0-12cm diameter range under the plant, which indicated that the root under MT and AT were more concentrated under the plant. 5) Root activity was DS >MT>AT before transplanting with a extremely significant difference; the root activity of MT and AT increased rapidly after transplanting with no significant difference after recovery; root bleeding intensity under DS, MT and AT at 35d after heading decreased by 84.7%, 75.4% and 74.3%, respectively compared with 0 d after heading for Yixiangyou 2115, and it decreased by 79.3%, 75.9% and 74.3%, respectively for Fyou 498; the root senescence of DS was faster. In general, the effect of mechanical planting on root traits of indica hybrid rice was significant, the roots under MT in the heading stage distributed shallowly, and the root was thick with a larger root number; the roots under MT distributed shallowly, with the least root diameter and the most root tips, root senescence was the fast after heading stage; the roots under MT distributed deeply, and the root was thick with a smaller root number.