The observation minus reanalysis (OMR) method is widely used to investigate the impact of urbanization and land use change on climate. Here we present the OMR trends for the periods of 1979–1998 and 1989–2008 in eastern China, which appear inconsistent for the regions experiencing rapid urbanization during recent decades. Using Ensemble Empirical Mode Decomposition, we extract the secular trend and multidecadal variability (MDV) from the temperature observations at stations and the corresponding reanalysis data for the last century and find that, in general, MDV in the reanalysis data is weaker than that in the station observations. This systematic difference considerably modulates the magnitude of the OMR trends during different periods, leading to inconsistent estimates of the impact of urbanization. After MDV adjustment, the OMR trends for Beijing and Shanghai are consistent for the different periods, about 0.04°C–0.1°C/decade, much smaller than some previous estimates. We caution those using OMR methods to estimate the effect of urbanization and also for those using reanalysis data for a limited period in studies of this kind.