In irradiated tungsten (W), the formation of numerous helium (He) bubbles has a significant impact on the diffusion behaviors of hydrogen (H) isotopes. To investigate the influence of the microstructure of He bubbles on the diffusion behaviors of deuterium (D), we utilize the reconstructed experimental data, the phase-field method, and the steady-state diffusion equation to calculate the effective diffusion coefficients of D based on four possible diffusion paths, i.e., D atoms diffuse in the bulk W, inside the He bubbles, and along the outer and inner surface of He bubbles. Simulation results based on the reconstructed depth-dependent distribution of He bubbles reveal that the diffusion paths remarkably affect the effective diffusion coefficient of D. By varying the radius and number density of He bubbles, the effective diffusion coefficient of D undergoes significant changes. Subsequently, we fit an empirical formula of the effective diffusion coefficient of D as a function of the radius and number density of He bubbles for different diffusion paths of D based on simulation data. Besides, the growth behaviors of He bubbles are simulated by the phase-field model, and the effective diffusion coefficient of D as a function of the evolutionary time for different diffusion paths is also discussed. At last, we investigate the influence of the D concentration and temperature on the effective diffusion coefficient of D along different diffusion paths. These results indicate that the effective diffusion coefficient of D increases with decreasing the D concentration and increasing the temperature for four diffusion paths. The current study provides a reference for investigating the diffusion behaviors of D in W in the presence of He bubbles, and may benefit the efforts of developing low D retention W-based materials.