Although several studies have focused on the adaptations provided by inspiratory muscle (IM) training on physical demands, the warm-up or pre-activation (PA) of these muscles alone appears to generate positive effects on physiological responses and performance. This study aimed to understand the effects of inspiratory muscle pre-activation (IMPA) on high-intensity running and passive recovery, as applied to active subjects. In an original and innovative investigation of the impacts of IMPA on high-intensity running, we proposed the identification of the interactions among physical characteristics, physiological responses and muscle oxygenation in more and less active muscle to a running exercise using a complex network model. For this, fifteen male subjects were submitted to all-out 30 s tethered running efforts preceded or not preceded by IMPA, composed of 2 × 15 repetitions (1 min interval between them) at 40% of the maximum individual inspiratory pressure using a respiratory exercise device. During running and recovery, we monitored the physiological responses (heart rate, blood lactate, oxygen saturation) and muscle oxygenation (in vastus lateralis and biceps brachii) by wearable near-infrared spectroscopy (NIRS). Thus, we investigated four scenarios: two in the tethered running exercise (with or without IMPA) and two built into the recovery process (after the all-out 30 s), under the same conditions. Undirected weighted graphs were constructed, and four centrality metrics were analyzed (Degree, Betweenness, Eigenvector, and Pagerank). The IMPA (40% of the maximum inspiratory pressure) was effective in increasing the peak and mean relative running power, and the analysis of the complex networks advanced the interpretation of the effects of physiological adjustments related to the IMPA on exercise and recovery. Centrality metrics highlighted the nodes related to muscle oxygenation responses (in more and less active muscles) as significant to all scenarios, and systemic physiological responses mediated this impact, especially after IMPA application. Our results suggest that this respiratory strategy enhances exercise, recovery and the multidimensional approach to understanding the effects of physiological adjustments on these conditions.