Weyl semimetal Td‐MoTe2 has recently attracted much attention due to its intriguing electronic properties and potential applications in spintronics. Here, Fe‐intercalated Td‐FexMoTe2 single crystals (0 < x < 0.15 ) are grown successfully. The electrical and thermoelectric transport results consistently demonstrate that the phase transition temperature TS is gradually suppressed with increasing x. Theoretical calculation suggests that the increased energy of the Td phase, enhanced transition barrier, and more occupied bands in 1T′ phase is responsible for the suppression in TS. In addition, a ρα–lnT behavior induced by Kondo effect is observed with x ≥ 0.08, due to the coupling between conduction carriers and the local magnetic moments of intercalated Fe atoms. For Td‐Fe0.15MoTe2, a spin‐glass transition occurs at ≈10 K. The calculated band structure of Td‐Fe0.25MoTe2 shows that two flat bands exist near the Fermi level, which are mainly contributed by the dyz and dx2−y2${{\rm{d}}_{{x^2} - {y^2}}}$ orbitals of the Fe atoms. Finally, the electronic phase diagram of Td‐FexMoTe2 is established for the first time. This work provides a new route to control the structural instability and explore exotic electronic states for transition‐metal dichalcogenides. Fe‐intercalated Td‐FexMoTe2 single crystals (0 ≤ x ≤ 0.15) are grown successfully. The Fe intercalation significantly tunes the structural instability and brings about exotic electronic properties for the Weyl semimetal MoTe2, including the first observed Kondo effect and spin‐glass transition in its topologically nontrivial Td phase at low temperature.