We demonstrate four-wave mixing (FWM) in the graphdiyne (GDY) microfiber based on the synchronized dual-wavelength pump pulses that are transformed from a mode-locked fiber laser. Benefiting from the large nonlinear refractive index of GDY and the synchronized pump pulses, a maximum conversion efficiency of -39.05 dB can be achieved in GDY with only an average pump power of 6.9 mW, greatly alleviating the possible damage compared to previous investigations employing the continuous-wave pump. In addition, our proposal can be applied to measure the effective nonlinear coefficient $\gamma$ of the GDY-microfiber, which could be extended as a practical measurement tool for $\gamma$ of nanomaterials-based devices.