Drought monitoring is one of the significant issues of water resources assessment. Multiple drought indices (DIs), including Percent of Normal (PN), Standardized Precipitation Index (SPI), statistical Z-Score, and Effective Drought Index (EDI) at 18 different timesteps were employed to evaluate the drought condition in Wuyuer River Basin (WRB), Northeast China. Daily precipitation data of 50 years (1960–2010) from three meteorological stations were used in this study. We found DIs with intermediate time steps (7 to 18 months) to have the highest predictive values for identifying droughts. And DIs exhibited a better similarity in the 12-month timestep. Among all the DIs, EDI exhibited the best correlation with other DIs for various timesteps. When further comparing with historical droughts, Z-Score, SPI, and EDI were found more sensitive to multi-monthly cumulative precipitation changes (r2 > 0.55) with respect to monthly precipitation changes (r2 ≤ 0.10), while EDI was more preferable when only monthly precipitation data were available. These results indicated that various indices for different timesteps should be investigated in drought monitoring in WRB, especially the intermediate timesteps should be considered.