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This study was designed to analyze the genetic relationship of the morphological traits of the northern japonica hybrid rice. The genetic relationship of the morphological traits of the 100 cultivars combined by the 10 sterile lines and the 10 restore lines was studied by using the principle component analysis and the SAS and QGA. The results showed that compared with the female parent, most of the morphological traits related closely to their father. The additive genetic effect and the dominant genetic effect appeared significantly, and the former was more significant than the latter. Genetic correlation analysis indicated that high plants or high plants with more leaves were in favor of improving the number and the weight of the spike and producing the hybrid vigor. The important factors influencing the plant type of the northern japonica hybrid rice were the plant height (PH), the angle of the flag leaf (FLA), flag leaf length (FLL), and the weight of the shoots and leaves (SLW), respectively. The morphological traits system of the northern japonica hybrid rice was very complex, and the restore line should be given more importance compared with the sterile line, and PH, FLA, FLL, and SLW should be considered first in the plant type breeding.