Soil salinization is a global issue resulting in soil degradation, arable land loss and ecological environmental deterioration. Over the decades, multispectral and hyperspectral remote sensing have enabled efficient and cost-effective monitoring of salt-affected soils. However, the potential of hyperspectral sensors installed on an unmanned aerial vehicle (UAV) to estimate and map soil salinity has not been thoroughly explored. This study quantitatively characterized and estimated field-scale soil salinity using an electromagnetic induction (EMI) equipment and a hyperspectral camera installed on a UAV platform. In addition, 30 soil samples (0~20 cm) were collected in each field for the lab measurements of electrical conductivity. First, the apparent electrical conductivity (ECa) values measured by EMI were calibrated using the lab measured electrical conductivity derived from soil samples based on empirical line method. Second, the soil salinity was quantitatively estimated using the random forest (RF) regression method based on the reflectance factors of UAV hyperspectral images and satellite multispectral data. The performance of models was assessed by Lin’s concordance coefficient (CC), ratio of performance to deviation (RPD), and root mean square error (RMSE). Finally, the soil salinity of three study fields with different land cover were mapped. The results showed that bare land (field A) exhibited the most severe salinity, followed by dense vegetation area (field C) and sparse vegetation area (field B). The predictive models using UAV data outperformed those derived from GF-2 data with lower RMSE, higher CC and RPD values, and the most accurate UAV-derived model was developed using 62 hyperspectral bands of the image of the field A with the RMSE, CC, and RPD values of 1.40 dS m−1, 0.94, and 2.98, respectively. Our results indicated that UAV-borne hyperspectral imager is a useful tool for field-scale soil salinity monitoring and mapping. With the help of the EMI technique, quantitative estimation of surface soil salinity is critical to decision-making in arid land management and saline soil reclamation.