Brassinosteroids (BRs) are important plant hormones regulating plant growth and development. High-performance analytical methods for quantifying endogenous BRs are important for studying the molecular mechanisms of BR action. Herein we developed a high-performance sample pretreatment method based on boronate affinity magnetic nanoparticles (BAMNPs). The high specificity of boronate affinity enables direct fishing of BRs from plant matrices. The strong binding energy makes it possible to remove most contaminants in plant matrices with a small loss of target BRs. Besides these advantages, the novel two-step oxidation-hydrolysis elution system raised BR recoveries to 70.5%–98.2%, which was much higher than other boronate affinity applications. The high cleanliness of the final eluents lowered the matrix effects to 85.2%–92.4%. As a result, this method enables simultaneously good recoveries of endogenous BRs and thorough removal of matrix interferences, which greatly improves the sensitivity of BR analysis and reduces the use of plant materials for routine analysis to <10 mg. In addition, the sample handling time can be shortened to <3 h due to the operating convenience of BAMNPs and their easy separation from plant powders. Based on these advantages of BAMNP solid phase extraction, the organ-specific BR distribution analysis in Arabidopsis and rice tissues demonstrates excellent sensitivity, good reproducibility and high throughput of the method.