Flexor tendons function as energy storage and shock absorption structures in the tarsometatarso-phalangeal joint (TMTPJ) of ostrich feet during high-speed and heavy-load locomotion. In this study, mechanisms underlying the energy storage and shock absorption of three flexor tendons of the third toe were studied using histology and scanning electron microscopy (SEM). Macroscopic and microscopic structures of the flexor tendons in different positions of TMTPJ were analyzed. Histological slices showed collagen fiber bundles of all flexor tendons in the middle TMTPJ were arranged in a linear-type, but in the proximal and distal TMTPJ, a wavy-type arrangement was found in the tendon of the M. flexor digitorum longus and tendon of the M. flexor perforans et perforatus digiti III, while no regular-type was found in the tendon of the M. flexor perforatus digiti III. SEM showed that the collagen fiber bundles of flexor tendons were arranged in a hierarchically staggered way (horizontally linear-type and vertically linear-type). Linear-type and wavy-type both existed in the proximal TMTPJ for the collagen fiber bundles of the tendon of the M. flexor perforatus digiti III, but only the linear-type was found in the distal TMTPJ. A number of fibrils were distributed among the collagen fiber bundles, which were likely effective in connection, force transmission and other functions. The morphology and arrangement of collagen fiber bundles were closely related to the tendon functions. We present interpretations of the biological functions in different positions and types of the tendons in the TMTPJ of the ostrich feet.