Understanding the properties of cracked rocks is of great importance in scenarios involving CO2 geological sequestration, nuclear waste disposal, geothermal energy, and hydrocarbon exploration and production. Developing noninvasive detecting and monitoring methods for such geological formations is crucial. Many studies show that seismic waves exhibit strong dispersion and attenuation across a broad frequency range due to fluid flow at the pore scale known as squirt flow. Nevertheless, how and to what extent squirt flow affects seismic waves is still a matter of investigation. To fully understand its angle- and frequency-dependent behavior for specific geometries, appropriate numerical simulations are needed. We perform a three-dimensional numerical study of the fluid–solid deformation at the pore scale based on coupled Lamé–Navier and Navier–Stokes linear quasistatic equations. We show that seismic wave velocities exhibit strong azimuth-, angle- and frequency-dependent behavior due to squirt flow between interconnected cracks. Furthermore, the overall anisotropy of a medium mainly increases due to squirt flow, but in some specific planes the anisotropy can locally decrease. We analyze the Thomsen-type anisotropic parameters and adopt another scalar parameter which can be used to measure the anisotropy strength of a model with any elastic symmetry. This work significantly clarifies the impact of squirt flow on seismic wave anisotropy in three dimensions and can potentially be used to improve the geophysical monitoring and surveying of fluid-filled cracked porous zones in the subsurface.