Abstract: For verifying application of AutoCAD in measuring anatomy structure of branch in apple rootstock, how to measure the length and area of tissue in anatomy structure of 2-year apple dwarf rootstock Y-1 by AutoCAD was introduced by giving an example. The precision of IPE method and AutoCAD method was compared by measuring the length of accurate 1mm and 1mm2, and the significance of difference in measuring value of the 2 methods were analyzed by measuring the tissue thickness and area of vessel in different position and sieve tube area in anatomy structure of 2-year apple dwarf rootstock Y-1, using 2 methods separately. The results showed that AutoCAD method is more accurate than IPE method, the difference of measuring value with the 2 methods is not significant. It conclude that AutoCAD method is more accurate, convenient, strong functional than IPE method in measuring the length and area of tissue of anatomy structure of branch in apple rootstock, it put forward that measuring the length and area of tissue of anatomy structure of branch in apple rootstock by AutoCAD method is deserved to recommend, and may be applied in micromeasurement of other plants.