Safflower (Carthamus tinctorius L.) is one of the most important crop plants that has been utilized for production of oleosins. miRNAs (microRNAs) are a class of small and non-coding RNAs that negatively regulate gene expression at post-transcriptional level thus playing a role in plant growth, development, and stress response. In this study, high-throughput Illumina sequencing technology has been used to comprehensively investigate the small RNA transcriptomes of safflower seed, flower, and leaf. It is found that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression abundance exhibited evolutionary conservation across multiple plants. Comparison of their expression abundance among different tissues shows that a total of 116, 133, and 128 miRNAs are significantly differentially expressed with higher abundance or lower abundance between safflower seed/leaf, seed/petal, and leaf/petal. The majority of the most significant differences in miRNA abundance between tissues are tissue-specific miRNAs. In addition, 13 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.