Owing to their broad range of redox potential, quinones/hydroquinones can be utilized for energy storage in redox flow batteries. In terms of stability, organic catholytes are more challenging than anolytes. The two-electron transfer feature adds value when building all-quinone flow battery systems. However, the dimerization of quinones/hydroquinones usually makes it difficult to achieve a full two-electron transfer in practical redox flow battery applications. In this work, we designed and synthesized four new hydroquinone derivatives bearing morpholinomethylene and/or methyl groups in different positions on the benzene ring to probe molecular stability upon battery cycling. The redox potential of the four molecules were investigated, followed by long-term stability tests using different supporting electrolytes and cell cycling methods in a symmetric flow cell. The derivative with two unoccupied ortho positions was found highly unstable, the cell of which exhibited a capacity decay rate of ~50% per day. Fully substituted hydroquinones turned out to be more stable. In particular, 2,6-dimethyl-3,5-bis(morpholinomethylene)benzene-1,4-diol (asym-O-5) displayed a capacity decay of only 0.45%/day with four-week potentiostatic cycling at 0.1 M in 1 M H3PO4. In addition, the three fully substituted hydroquinones displayed good accessible capacity of over 82%, much higher than those of conventional quinone derivatives.