Dead flower buds were frequently observed in the Japanese pear cultivar 'Kosui' (Pyrus pyrifolia) when trees were cultured under open field conditions in the southwestern regions of Japan. To elucidate the causes of dead flower buds, we studied the effect of nitrogen (N) supplements using two experimental designs that included trees grown in pots and in the field. First, we investigated the effect of applying chemical N fertilizer during the winter using potted trees (controlled temperature experiment). We also investigated the effect of applying livestock waste compost during the fall-winter months on flower bud freezing tolerance and on the N and sugar contents of flower buds from trees cultivated in the field. In controlled temperature conditions, the percentage of dead flower buds significantly increased when N fertilizer was applied in December and January. In field conditions, compost application in the fall-winter months significantly reduced the freezing tolerance of flower buds concomitant with a significant increase in the percentage of dead flower buds compared to compost application in the spring. Application of compost in the fall-winter months resulted in a significantly higher N content compared to that in spring. In contrast, the relationship between the sugar content and freezing tolerance of flower buds is unclear. This potential connection remains to be elucidated in the near future. Collectively, these results suggest that compost application during the fall-winter season can adversely affect freezing tolerance through an increase in the N content, thus promoting dead flower buds.