In this paper, two quinoxaline-based small organic molecules, which are conjugated and mutual isomers in vertical and horizontal directions, were successfully synthesized. By exploring isomers with identical functional groups, the impact from changing in molecular composition on the observed different performance can be minimized. Their photoelectrical properties, thin-film morphology and the electrical memory performance were comparatively investigated. The devices based on these two small molecules both showed ternary WORM storage performance. Compared with vertical direction, horizontal molecule had a lower threshold voltage and higher current ratio. The results of AFM and XRD showed that horizontal molecule has better thin-film morphology and layered accumulation, which are conducive to the migration of carriers. We hope this study can provide a new reference to the future elaborate design and synthesis of novel small-molecule electrical memory materials.