We have developed a novel ultrasensitive online analytical system which integrated solid-phase-based extraction (SPBE) techniques with ultra-high performance liquid chromatography (UPLC) based on a fractionized sampling and stacking (FSS) strategy. FSS was proposed as a novel peak compression strategy to prevent band broadening and distortion caused by excessive solvents with high elution strength, which has been a main obstacle to conjunction of sample preparation techniques with UPLC. Such a strategy was based on online dividing a sample solution into fractions by plugs of weak mobile phase, followed by head-column stacking process, aiming to obtain a quite sharp sample zone. FSS enables UPLC to tolerate much larger injection volume of solvents with high elution strength, which facilitates hyphenation of SPBE with UPLC without peak distortion or loss of sensitivity. On the basis above, an online SPBE-UPLC system was realized by FSS, and its applicability was preliminarily verified by the successful development of a sensitive solid phase extraction-FSS-UPLC method for the determination of triazines. Subsequently an integrated online system incorporating molecularly imprinted in-tube solid phase microextraction, derivatization and FSS-UPLC was developed for the analysis of ultra trace 24-epibrassinolide. The developed method was ultrasensitive with detection limit as low as 0.7 ng/L, and the linear range of the method was 3–5000 ng/L. The endogenous 24-epibrassinolide in pollen, flower and seed samples was determined, which showed satisfactory recoveries in the range of 81.2–116% and good precision with relative standard deviation (RSD) values between 4.7 and 9.7%. This online analytical method was sensitive, reliable, rapid and applicable to trace analysis in complex samples.