As the output power increases, the transverse mode instability (TMI) has become a major limitation for power scaling of high power fiber lasers with nearly diffraction-limited beam quality. Many strategies in experimental or theoretical scopes have been proposed to mitigate the TMI. Theoretical studies have indicated that the TMI thresholds of the laser amplifiers are affected by the seed laser wavelength. In this work, the influences of seed wavelengths on the TMI threshold in high power large-mode-area ytterbium-doped fiber (YDF) amplifiers based on an all-fiber master oscillation power amplifier structure are investigated experimentally. The TMI characteristics and thresholds of the same fiber amplifier seeded by respective 1080 nm, 1070 nm, and 1065 nm fiber lasers are analyzed and compared. The experimental results show that the TMI threshold decrease with the seed wavelength in the region of 1065 nm–1080 nm. For every 5 nm decrease in seed wavelength, the TMI threshold power can be increased by about 290 W. Compared with the fiber amplifier of the 1080 nm seed wavelength, the TMI thresholds of the 1070 nm and 1065 nm wavelength fiber amplifiers are respectively increased by around 58.7% and 86.2%. Reducing the wavelength of seed can effectively improve the TMI threshold, but the amplified spontaneous emission (ASE) and nonlinear effects are also enhanced. The results have significant guidance for the mitigation of TMI in high-power YDF laser systems.