Organic materials have long been recognized as resource-abundant, sustainable, and potentially low-cost electrode materials that will handily satisfy the ever-growing demand for batteries. Although once had the reputation as being less stable and kinetically slow compared with their traditional inorganic counterparts, organic materials have been steadily improving on performance to be competent electrode candidates in recent years. We have recently reported a π-conjugated redox polymer with high cycling stability, high capacity utilization, and ultra-fast Li storage kinetics. The polymer delivers 80% of its theoretical capacity at a rate of 50C even with a high active mass ratio of 80 wt.% at practical mass loading, which is unusual for organic electrode materials. There is no established theory as for how such performance can be achieved and optimized via molecular design and microstructure engineering. We set out to scrutinize the charge storage mechanism of polymer electrodes and investigate the influence of molecular electronic structure and electrode microstructure on electrochemical performance. We have designed and synthesized a series of polymers with similar molecular structure but varying degree of conjugation in the backbone. The polymers are evaluated as Li storage electrode materials. The morphology and its evolution, charge transfer process, and state-of-charge-dependent electron and ion transport of the polymer electrodes are monitored and correlated to the cell performance. We found that regardless of the degree of conjugation, the redox reaction and the bulk ionic diffusion in the polymers proceed at comparable rates. We developed a procedure to directly measure the electrical conductivity of electrochemically lithiated polymers. This conductivity increases by 100-fold as the π-conjugation degree of the polymers increases. The structural order and morphology of the polymers differ widely with the conjugation length, leading to significantly different microstructure. The electrochemical surface area of the polymer electrode is continuously altered by the π-conjugation degree, which in turn impacts the ion transport model in the electrode. Overall, our study establishes general analysis tools that elucidate the underlying charge storage mechanism of polymer electrode materials. The results shown here provide guidance for further advancing high-energy/power energy battery based on organic materials.