Ventilated acoustic resonator(VAR), a type of acoustic metamaterial, emerge as an alternative for sound attenuation in environments that require ventilation, owing to its excellent low-frequency attenuation performance and flexible shape adaptability. However, due to the non-linear acoustic responses of VARs, the VAR designs are generally obtained within a limited parametrized design space, and the design relies on the iteration of the numerical simulation which consumes a considerable amount of computational time and resources. This paper proposes an acoustic response-encoded variational autoencoder (AR-VAE), a novel variational autoencoder-based generative design model for the efficient and accurate inverse design of VAR even with non-parametrized designs. The AR-VAE matches the high-dimensional acoustic response with the VAR cross-section image in the dimension-reduced latent space, which enables the AR-VAE to generate various non-parametrized VAR cross-section images with the target acoustic response. AR-VAE generates non-parameterized VARs from target acoustic responses, which show a 25-fold reduction in mean squared error compared to conventional deep learning-based parameter searching methods while exhibiting lower average mean squared error and peak frequency variance. By combining the inverse-designed VARs by AR-VAE, multi-cavity VAR was devised for broadband and multitarget peak frequency attenuation. The proposed design method presents a new approach for structural inverse-design with a high-dimensional non-linear physical response.