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The phenomenon of secondary electron emission is of considerable interest in areas such as particle accelerators and on-board radio frequency (RF) components. Total secondary electron yield (TSEY) is a parameter that is frequently used to describe the secondary electron emission capability of a material. It has been widely recognized that the TSEY vs. primary electron energy curve has a single-hump shape. However, the TSEY–energy curve with a double-hump shape was also observed experimentally—this anomaly still lacks explanation. In this work, we explain this anomaly with the help of a millimetre-scale (mm-scale) silver pillar array fabricated by three-dimensional (3D) printing technology. The TSEY–energy curve of this pillar array as well as its flat counterpart is obtained using sample current method. The measurement results show that for the considered primary electron energy (40–1500 eV), the pillar array can obviously suppress TSEY, and its TSEY–energy curve has an obvious double-hump shape. Through Monte Carlo simulations and electron beam spot size measurements, we successfully attribute the double-hump effect to the dependence of electron beam spot size on the primary electron energy. The observations of this work may be of help in determining the TSEY of roughened surface with characteristic surface structures comparable to electron beam spot size. It also experimentally confirms the TSEY suppression effect of pillar arrays.