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Amyotrophic lateral sclerosis (ALS) is a progressive nervous system disease that causes motor neuron (MN) degeneration and results in patient death within a few years. To recapitulate the cytopathies of ALS patients’ MNs, <i>SOD1</i>^G85R mutant and corrected <i>SOD1</i>^G85G isogenic-induced pluripotent stem cell (iPSC) lines were established. Two <i>SOD1</i> mutant ALS (<i>SOD1^G85R</i> and <i>SOD1</i>^D90A), two <i>SOD1</i> mutant corrected (<i>SOD1</i>^G85G and <i>SOD1</i>^D90D), and one sporadic ALS iPSC lines were directed toward MNs. After receiving ~90% purity for MNs, we first demonstrated that <i>SOD1</i>^G85R mutant ALS MNs recapitulated ALS-specific nerve fiber aggregates, similar to <i>SOD1</i>^D90A ALS MNs in a previous study. Moreover, we found that both <i>SOD1</i> mutant MNs showed ALS-specific neurite degenerations and neurotransmitter-induced calcium hyperresponsiveness. In a small compound test using these MNs, we demonstrated that gastrodin, a major ingredient of <i>Gastrodia elata</i>, showed therapeutic effects that decreased nerve fiber cytopathies and reverse neurotransmitter-induced hyperresponsiveness. The therapeutic effects of gastrodin applied not only to <i>SOD1</i> ALS MNs but also to sporadic ALS MNs and <i>SOD1</i>^G93A ALS mice. Moreover, we found that coactivation of the GSK3β and IGF-1 pathways was a mechanism involved in the therapeutic effects of gastrodin. Thus, the coordination of compounds that activate these two mechanisms could reduce nerve fiber cytopathies in <i>SOD1</i> ALS MNs. Interestingly, the therapeutic role of GSK3β activation on <i>SOD1</i> ALS MNs in the present study was in contrast to the role previously reported in research using cell line- or transgenic animal-based models. In conclusion, we identified in vitro ALS-specific nerve fiber and neurofunctional markers in MNs, which will be useful for drug screening, and we used an iPSC-based model to reveal novel therapeutic mechanisms (including GSK3β and IGF-1 activation) that may serve as potential targets for ALS therapy.