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As a noninvasive neuromodulation technique, transcranial magnetic stimulation (TMS) offers insights into motor system physiology through motor-evoked potentials (MEPs). In the present study, we applied a factorization approach to multimuscle MEPs to characterize the pattern-level structure of corticospinal outputs beyond conventional per-muscle amplitude measures. To evaluate this approach, we analyzed multimuscle MEP datasets from three experiments in healthy young adults focusing on different stimulus parameters: stimulus intensity ( experiment 1: n = 40), motor mapping size ( experiment 2: n = 35), and activation of intracortical circuits by a paired-pulse TMS paradigm ( experiment 3: n = 20). We extracted motor-evoked modules (MEMs) using non-negative matrix factorization (NMF) and compared their structure across different stimulus conditions. MEM structure was impacted by stimulus intensity, and these findings indicate that stimulus intensity shapes the pattern-level structure of corticospinal outputs. Varying motor mapping size had only a minor impact on MEM structure, suggesting that the pattern-level structure of corticospinal outputs elicited by TMS was stable across mapping extents. Activation of intracortical inhibition appeared to alter MEM structure compared with single-pulse TMS. These findings suggest that paired-pulse activation of intracortical inhibition may alter the pattern-level structure of corticospinal outputs. The MEM framework allows us to characterize the pattern-level structure of corticospinal outputs beyond single-muscle MEPs; thus, MEMs obtained from TMS complement well-established single-muscle MEP analyses and offer a novel perspective for investigating the motor system.