Under a changing environment, the effect of climate change and human activities on maize yield is vital for ensuring food security and efficient socio-economic development. The time series of maize yield is generally non-stationary and contains different frequency components, such as long- and short-term oscillations. Nevertheless, there is no adequate understanding of the relative importance of climate change. In addition, human activities on maize yield at multiple timescales remain unclear, which help in further improving maize yield prediction. Based on the ensemble empirical mode decomposition method (EEMD), the method of dependent variable variance decomposition (DVVD) and the Sen-slope method, the effect of climate change including growing-season precipitation and temperature (i.e., GSP, GEP, CDD, GST, GSMAT, and GSMT) and human activities including effective irrigation area (EIA) and the consumption of chemical fertilizers (CCF) on maize yield were explored at multiple timescales during 1979–2015. The Heilongjiang Province, a highly important maize production area in China, was selected as a case study. The results of this work indicate the following: (1) The original maize yield series was divided into 3.1-, 7.4-, 18.5-, and 37-year timescale oscillations and a residual series with an increasing trend, where the 3.1-year timescale (IMF1), the 18.5-year timescale (IMF3), and the increasing trend (R) were dominant; (2) the original sequence was mainly affected by human activities; (3) climate change and human activities had different effects on maize yield at different timescales: The short-term oscillation (IMF1) of maize yield was primarily affected by climate change. However, human activities dominated the mid- and long-term oscillations (IMF3 and R) of maize yield. This study sheds new insight into multiple timescale analysis of the role of climate and human activities on maize yield dynamics.