As an effective supplement to ground machinery, UAVs play an important role in agriculture and have become indispensable intelligent equipment in the development of precision agriculture. Various types of agricultural UAV-based spreading devices, mainly disc-type and pneumatic-type, have appeared in domestic and foreign markets. UAV-based rice topdressing has gradually become a widely recognized application with great market potential. In the process of UAV-based low-altitude fertilization, due to the existence of the rotor wind field, the environment for particle air diffusion is complex, and the movement trajectory and deposition distribution of fertilizer are affected by many factors, resulting in large differences in the spreading. The flight height and speed have a great influence on particle movement and deposition, and a reasonable combination of work parameters can be used for efficient and high-quality particle deposition. In order to obtain better particle deposition distribution, this paper uses the method of a single flight line to test and analyze the characteristics of particle deposition distribution for fertilization using multi-rotor UAVs at different flight heights and speeds. The effective swath width and deposition uniformity obtained via the simulation of overlapped route superposition were used to optimized the appropriate work parameters to ensure that a reasonable and effective deposition amount can be obtained during actual application. The results show that the flight height and speed and the interaction of both have an important influence on the deposition amount and the effective width, but it is not a simple linear relationship. On the whole, as the flight height increases, the coefficient of variation decreases and the effective width increases, but it is not obvious when the speed is low. For the R20, when the flight speed is 2 m/s, the effective width first increases and then decreases with the increase in flight height, and the difference in the deposition amount at a height of 5 m is larger than that at other heights. Under the three working heights, the effective swath width is the same when the flight speed is 4 m/s and 6 m/s, and the effective swath width is also the same when the speed is 7 m and 9 m. For the T16, when the flight speed is 4 m/s, the deposition uniformity is relatively good, and the effective width increases with the increase in flight height. Therefore, the combination of 7–6 m/s and 9–4 m/s parameters will be the best operating parameters for R20 and T16. However, considering the actual dynamic meteorological environment in the field, the operating height can be appropriately lowered according to the influence of the crosswind during actual operation. The research results of this paper can provide scientific reference and suggestions for further improving the effect of UAV-based fertilization.