(1) Background: Exploring the relationship between spontaneous breathing patterns and aerobic and anerobic running exercise performance can greatly improve our understanding of optimizing physical fitness. Spontaneous breathing patterns refer to how the rhythm and depth of breathing affect performance and physical adaptation during exercise. (2) Methods: This study aimed to investigate this relationship by enrolling 240 college students (120 males and 120 females, aged 18–22). We evaluated their resting respiratory rate (RR), the combined total of abdominal and thoracic movements (AM+TM), the proportion of abdominal movement to the overall respiratory movement (AM/(AM+TM)), and the inhalation to exhalation ratio (I/E ratio). Additionally, their performance in a 50 m sprint (measuring anerobic capability), an 800- or 1000 m run (assessing mixed aerobic and anerobic capacity), and a 12 min distance run (evaluating aerobic capacity) was recorded. (3) Results: Our findings, through both correlational and comparative analyses, indicate that a larger AM+TM is predictive of a greater distance covered in the 12 min run, suggesting enhanced aerobic capacity. Interestingly, among female participants, a lower body mass index (BMI) coupled with a higher proportion of abdominal movement (AM/(AM+TM)) was linked to better performance in the 800 m run, indicative of superior mixed aerobic and anerobic capacities. These results imply that women with a larger tidal volume and those with a lower BMI but higher abdominal contribution to breathing at rest may exhibit better aerobic and mixed exercise capacities, respectively. (4) Conclusions: Based on these findings, we recommend that healthcare professionals and physical education instructors incorporate respiratory pattern assessments into their practices to potentially improve the physical health of their clients and students, with a particular emphasis on female populations. This study underscores the importance of understanding the intricate relationship between spontaneous respiratory patterns and exercise capabilities in enhancing overall physical fitness and health.