Upscaling in situ soil moisture observations (ISMO) to multiscale pixel estimations with kriging is a key step in the comprehensive usage of ISMO and remote sensing (RS) soil moisture data. Scale effects occur and introduce uncertainties during upscaling processes because of spatial heterogeneity and the kriging method. A nested hierarchical scale series was established at the field level, and upscaled estimations at each scale were obtained by block kriging (BK) to illustrate multiscale ISMO upscaling processes. Those uncertainties were described with the results of comparison analysis against RS data, statistical analysis, and spatial trend surface analysis on multiscale estimations and were explained from the spatial heterogeneity perspective with a semivariogram analysis on ISMO. The results show that uncertainties exist and vary in multiscale upscaling processes, and the range of the empirical semivariogram could indicate scale effects. When the target scale is shorter than the range, BK maintains similar scale effects and global trends during upscaling processes, and the direct pixel estimation by BK is relatively close to the average of nested pixel estimations. This has great implications for understanding the kriging method in similar works.