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Genetic modification of Cry-proteins from Bacillus thuringiensis (Bt) is a common practice in economically important crops to improve insecticide resistance and reduce the use of pesticides. However, introduction of these genes can have unintended side effects, which should be closely monitored for effective breeding and crop management. To determine the potential cause of these negative effects, we explored assimilate partitioning in the transgenic Bt rice line T1c-19 (Cry1C*), which was compared with that of its wild-type counterpart Minghui 63 (MH63) under different potassium fertilization application treatment conditions. In a pot experiment, 0, 0.4, and 0.6 g K2O was applied per kg of dry soil to determine the phloem transport characteristics of the two rice lines. We used a variety of assessment indicators ranging from morphological to physiological aspects, including the number of large and small vascular bundles in the neck internode at the heading stage, the diameter and bleeding intensity of the neck internode at the filling stage, and the content and apparent ratio of transferred non-structural carbohydrates (NSC) in the culm and sheath from the heading to maturing stages. The K utilization and grain yield at the maturing stage were also concerned. Results presented that the mean setting rate and grain yield of T1c-19 (Cry1C*) decreased by 22.3% and 26.2% compared to those in MH63, respectively. Compared to MH63, the K concentration and accumulation were significantly higher in the culms and leaves, but significantly lower in grain of T1c-19 (Cry1C*). T1c-19 (Cry1C*) had less apparent NSC efflux in the culm and sheath, fewer small vascular bundles, and a smaller diameter and bleeding intensity of the neck internode than MH63. In addition, linear correlation analysis indicated that there were positive correlations among grain yield, setting rate, the apparent NSC efflux in the culm and sheath, number of small vascular bundles, and the neck internode diameter and bleeding intensity. These unintended effects may directly or indirectly be caused by insertion of exogenous Bt (Cry1C*) gene, which should be further considered in the future breeding of transgenic crops.