Wheat basic seedling number is one of the most important sources of the total number of wheat ears. In turn, the leading factor can also dominate the wheat yield per unit area. It is an essential prerequisite for the timely and accurate acquisition of the within-field spatial difference information of the wheat basic seedling number. The variable-rate topdressing of nitrogen fertilizer can then be implemented in the manner of precision agriculture. The population density of wheat tillers can often be regulated to realize the fertilizer reduction with a better yield. Unmanned Aerial Vehicle (UAV) remote sensing imagery can be efficiently obtained at the field level in recent years. However, the vegetation and background features can be only processed without considering the influence of mixed pixels of the imagery in the traditional agricultural UAV remote sensing applications. The accuracy and reliability of wheat basic seedling number inversion cannot fully meet the large-scale production in smart agriculture. In this study, the quantitative inversion accuracy of wheat basic seedling numbers was improved using the mixed pixel decomposition model of UAV remote sensing imagery. Firstly, the UAV remote sensing imagery was acquired with a spatial resolution of about 2.5 cm using DJI Mini drone. The relative radiometric calibration was then completed using the invariant target method. Furthermore, the endmembers of vegetation and soil, as well as the mixed pixels were extracted from the reflectance image, which accounted for 2.23%, 0.28%, and 97.49% of the pixels, respectively. The spectral signatures were acquired for the endmembers of vegetation and soil using the reflectance values. Consequently, the decomposition model was established using mixed pixels of UAV remote-sensing images. The linear decomposition was used to divide each mixed pixel into 2 components of vegetation and soil. The abundance data was acquired for each component. The vegetation abundance model was used to calculate the Fractional Vegetation Coverage (FVC) of the experimental field. The proportions of vegetation endmember and abundance were then evaluated over the total area of “1m and 2 rows”. Finally, a linear regression model was established between the FVC and the ground truth data of 15 sets of wheat basic seedling numbers. The determination coefficient R2 was 0.87. Besides, the regression model was verified using 3 other ground truth data of wheat basic seedling numbers. The verification results show that the Root Mean Square Error (RMSE) was 1.97 seedlings/m2. The higher inversing accuracy was achieved in this case, compared with the average wheat basic seedling number of 217.442 seedlings/m2 for the wheat field. A comparative experiment was performed on the FVC thematic maps. The traditional vegetation index method was used, including the Visible-band Difference Vegetation Index (VDVI), Green Red Difference Index (GRDI), and Green Red Ratio Index (GRRI). The linear regression models were then established between each FVC of VDVI, GRDI, GRRI, and ground truth data of wheat basic seedling number. The determination coefficient R2 and RMSE were calculated as 0.79, 0.56, 0.47, and 6.06, 7.04 and 4.43 seedlings/m2, respectively. Therefore, better performance was achieved in the quantitative inversion model of the wheat basic seedling number using the mixed pixels decomposition of UAV remote sensing images. The findings can provide data support for the precise variable topdressing of nitrogen fertilizer at the tillering stage of wheat.