In this paper, we investigate how traditional loop transformations affect flash memory performance. To do so, we propose cost models of loop structures in BAST (Block Associative Sector Translation) on flash memory. The proposed cost models reflect not only distinctive characteristics of flash memory but also loop structures, making these new models suitable to loop structures compared with previous cost models. Based on these cost models, we analyze the performance effects of loop transformation, and then determined the referenced order and stride variables which influence the performance in BAST. From the cost models and the experiments, we find out that loop distribution and loop fusion rarely affect performance, while that loop reversal and loop interchange apparently do, due to the one log block to one data block property of BAST. In addition, some loop transformations, when applied to flash memory based programs, can cause unexpected performance variations.