This study aimed to compare the intrinsic foot muscle (IFM) morphology and isometric strength among runners with habitual rearfoot strike (RFS) and non-rearfoot strike (NRFS) patterns. A total of 70 recreational male runners were included in this study (32 RFS and 38 NRFS), an ultrasound device and hand-held dynamometry were used to measure IFM morphology and isometric strength. Results indicated that the RFS runners had significantly thicker tibialis anterior (P = 0.01, ES = 0.64, 95% CI [0.01–0.07]) in IFMs morphology and higher Toe2345 flexion strength in IFMs strength (P = 0.04, ES = 0.50, 95% CI [0.01–0.27]) than NRFS runners, the cross-sectional area of flexor digitorum brevis was positively correlated with T2345 flexion strength (r = 0.33, p = 0.04), T12345 (r = 0.37, p = 0.02) and Doming (r = 0.36, p = 0.03) for runners with NRFS. IFMs morphology and isometric strength were associated with foot strike pattern, preliminary findings provide new perspectives for NRFS runners through the simple measurement of IFMs morphological characteristics predicting IFMs strength, future studies could adopt IFMs training to compensate the muscle strength defects and prevent foot-related injuries.