In this paper, a Japanese morphological analyzer for Japanese to Korean Machine Translation System is designed. The analyzer reconstructs the Japanese input sentence into word phrases that include grammatical and dictionary informations. Thus we propose the algorithm to separate morphemes and then connect them by reference to a corresponding Korean word phrases. And we define the connector to control Japanese word phrases It is used in controlling the start and the end point of the word phrase in the Japanese sentence which is without a space. The proposed analyzer uses the analysis dictionary to perform more efficient analysis than the existing analyzer. And we can decrease the number of its dictionary searches. Since the analyzer, proposed in this paper, for Japanese to Korean Machine Translation System processes each word phrase in consideration of the corresponding Korean word phrase, it can generate more accurate Korean expressions than the existing one which places great importance on the generation of the entire sentence structure.