Diagnosis of soil salinity and characterizing its spatial variability both vertically and horizontally are needed to establish control measures in irrigated agriculture. In this regard, it is essential that salinity development in varying soil depths be known temporally and spatially. Apparent soil electrical conductivity, measured by electromagnetic induction instruments, has been widely used as an auxiliary variable to estimate spatial distribution of field soil salinity. The main objectives of this paper were adopted a mobile electromagnetic induction (EMI) system to perform field electromagnetic (EM) survey in different soil layers, to evaluate the uncertainty through Inverse Distance Weighted (IDW) and Ordinary Kriging (OK) methods, and to determine which algorithm is more reliable for the local and spatial uncertainty assessment. Results showed that EM38 data from apparent soil electrical conductivity are highly correlated with salinity, more accurate for estimating salinity from multiple linear regression models, which the correlation coefficient of 0-20, 20-40, 40-60 and 60-80 cm were 0.9090, 0.9228, 0.896 and 0.9085 respectively. The comparison showed that the prediction accuracy of two methods also displays good performance for soil salinity, the estimation precision of IDW method (with E = 0.8873, 0.9075, 0.8483 and 0.901, RPD = 9.64, 8.01, 8.17 and 11.23 in 0-20, 20-40. 40-60 and 60-80 cm soil layers, respectively) was superior to that of OK (with E = 0.8857, 0.872, 0.8744 and 0.8822, RPD = 9.44, 7.83, 8.52 and 10.88, respectively), but differences of two methods in predictions are not significant. The obtained salinity map was helpful to display the spatial patterns of soil salinity and monitor and evaluate the management of salinity.