The greenhouse space is closed, and auxiliary pollination is needed to ensure the fruit setting rate and yield of tomatoes. Physical assisted pollination methods are green and healthy, with high fruit setting rate, and are the main pollination methods developed. Aiming at the problems of the existing physical assisted pollination methods, such as easy stem damage, large range of action and poor vibration effect, a pulse cluster pollination method was proposed and the corresponding pollination device was built. Through CFD simulation, the velocity distribution of nozzle flow field with single and double outlet number was obtained. With the range and fluid injection angle as evaluation indexes, the nozzle scheme with two outlet number and1 mm diameter of single hole was determined. Based on the gas-solid two-phase flow model, a CFD-DEM coupled simulation model was established to simulate the pollination process of tomato by observing the flowering morphology of tomato flower and analyzing its oscillation rule under the action of pulsed air flow. The orthogonal simulation of three factors and three levels was carried out with air blowing angle, air blowing frequency and air blowing distance as test factors and effective adhesion as evaluation index. The simulation results showed that the effect of various factors on the effective adhesion of pollen was in the order of blowing distance, blowing frequency and blowing angle. When the blowing distance was 182 mm, the blowing frequency was 24 Hz and the blowing angle was 76 °, the effective adhesion of pollen was the highest. At the same time, the simulation results were analyzed, and the pollination process of tomato flower under the action of pulse cluster method was obtained. The optimal parameter combination was used to test in a greenhouse. Compared with the test results, the maximum error of stigma pollen coverage was 5.54% and the average error was1.93%. Six weeks after pollination, the results of tomato fruit statistics showed that the fruit setting rate, single fruit weight and abnormal fruit rate were 82.81%, 229.60 g and 8.27%, which were better than that of other auxiliary pollination methods. The results showed that the coupling simulation model established was accurate and reliable, and it can provide a theoretical basis for the application of pulse cluster pollination method in intelligent devices. At the same time, it was verified that the pollination method can improve the fruit setting rate and yield of tomato, and meet the agronomic requirements of tomato pollination in greenhouse.