We have demonstrated a Yb-doped fiber laser (YDFL) based on a multifunctional acousto-optic tunable filter (AOTF) with flexible wavelength generation capability. The number of channels, as well as their diffracted wavelengths and corresponding peak transmittances of the AOTF, can be widely tuned by changing the composite drive signal from a homemade arbitrary wave generation (AWG) board enabling single-/multi-wavelength lasing with different central wavelengths and relative intensities. The maximal wavelength tuning range and minimal resolved wavelength spacing are ∼80nm and ∼1.5nm, respectively, with 3 dB bandwidth less than 0.15 nm for each laser line, showing great potential for further nonlinear frequency conversion. To the best of our knowledge, this is the first demonstration of flexible wavelength generation from a multifunctional AOTF-based YDFL directly driven by an AWG board.