The estimation of aircraft vertical acceleration response to atmospheric turbulence is fundamental to acceleration-based eddy dissipation rate (EDR) estimation. The linear turbulence field approximation with the wind gradients effects is utilized to describe the turbulence effects on civil aviation aircraft. To consider the wind gradients effects, the aircraft was modeled by a cruciform assembly in this study. A vertical acceleration estimation based on the unsteady vortex lattice method (UVLM) was proposed, in which the air-compression effects in high-subsonic flight were compensated by the Karman–Tsien rule. Results indicate that compared with the wing-tail assembly, the cruciform assembly with the wind gradients effects has better accuracy in computing acceleration response. The vertical acceleration response only induced by turbulence can be obtained for acceleration-based EDR estimation. Furthermore, with the optimized acceleration response, the estimated EDR value has got better accuracy and stability.