On-chip technology continuously explores and provides novel methods for high-throughput drug screening, such as droplet-array sandwiching technology. Droplet-array sandwiching technology involves upper and lower substrates with a droplet-array designed for a one-step process for drug screening, including cell-based screening. This technology is, however, limited to batch manipulation of the droplet-array. This paper proposes selective control of individual droplets, which allows different conditions for individual droplet pairs. Electrowetting-on-dielectric (EWOD) technology is introduced to control the height of the droplets so that the contact between droplet-pairs can be individually controlled. Circular patterns 4 mm in diameter composed of electrodes for EWOD and hydrophilic-hydrophobic patterns for droplet formation 4 μl in volume were developed. This paper presents and examines the selective control of the droplet height by EWOD for an applied voltage up to 160 V, followed by successful results of selective control of the contact and transport of substances.