The invention provides a decision tree based crop breeding evaluation method. The method comprises the following steps: a breeding objective is taken as the screening condition to establish a crop breeding evaluation data set which shares the same breeding objective, wherein each data in the data set is represented by a quaternary data type including an experimental material number, a property characteristic set T, an experiment e which the data belongs to as well as an experimental result r; the property characteristic sets T in the data set are pre-processed, and the data set after pre-processing is obtained; a model between the property characteristics and the experimental results is established by the decision tree according to the data set after pre-processing, and a decision tree based crop breeding evaluation model aiming at the breeding objective is obtained; character data of to-be-evaluated crops having the same breeding objective is analyzed according to the crop breeding evaluation model, and an evaluation result is obtained. With adoption of the method, the evaluation result information in the breeding process can be used to realize follow-up crop breeding evaluation.