The distribution characteristics of inorganic elements in plants play an important guiding role in the physiological, studies, which can reveal the distribution of nutrients, metabolic process, toxicity tolerance and other aspects in plants. Micro-XRF technology has many advantages to study inorganic elements, such as in situ, non-destructive, large area sample continuous mapping analysis, and simple pretreatment process. This study aims to explore the instrument parameters, pre-processing methods and data post-processing methods of micro-XRF in the distribution of inorganic elements of different plant organ samples. According to the difference of water content of different organs, we carried out different pretreatment schemes to obtain reliable experimental results. The influence of different point dwell time, chamber vacuum and other experimental conditions were compared. A variety of processing methods, such as image overlay, semi-quantitative analysis of concentration ratio of different elements, were carried out. The results show that micro-XRF technique has certain advantages in the determination of the distribution of inorganic elements in plant samples.