We present 2000 mock galaxy catalogues for the analysis of baryon acoustic oscillations (BAOs) in the Emission Line Galaxy (ELG) sample of the extended Baryon Oscillation Spectroscopic Survey Data Release 16 (eBOSS DR16). Each mock catalogue has a number density of 6.7 x 10(-4)h(3)Mpc(-3), covering a redshift range from 0.6 to 1.1. The mocks are calibrated to small-scale eBOSS ELG clustering measurements at scales of less than or similar to 30 h(-1) Mpc. The mock catalogues are generated using a combination of GaLAxy Mocks (GLAM) simulations and the quick particle-mesh (QPM) method. GLAM simulations are used to generate the density field, which is then assigned dark matter haloes using the QPM method. Haloes are populated with galaxies using a halo occupation distribution. The resulting mocks match the survey geometry and selection function of the data, and have slightly higher number density that allows room for systematic analysis. The large-scale clustering of mocks at the BAO scale is consistent with data and we present the correlation matrix of the mocks.