Measurement basis choice is an essential step in the underwater continuous variable quantum key distribution system based on homodyne detection. However, in practice, finite bandwidth of analog-to-digital converter on the receiver’s side is limited, which can result in defects in the measurement basis choice. That is, the receiver cannot accurately modulate the corresponding phase angle on the phase modulator for measurement basis choice to implement homodyne detection. The imperfect measurement basis choice will introduce extra excess noise, which affects the security of underwater continuous variable quantum key distribution scheme. To solve this problem, we propose an underwater continuous variable quantum key distribution scheme based on imperfect measurement basis choice, and analyze the influence of imperfect measurement basis choice on the performance of underwater continuous variable quantum key distribution system in detail. The research results indicate that the extra excess noise introduced by imperfect measurement basis choice can reduce the secret key rate and maximum transmission distance of the underwater Gaussian modulated quantum key distribution, thus reducing the security of the system. In order to achieve reliable underwater continuous variable quantum key distribution, we quantitatively analyze the extra excess noise introduced by choosing the imperfect measurement basis and obtain its security limit. Besides, we also consider the influence of different seawater depths on the security limit of the proposed scheme, effectively solving the security risks caused by the imperfect measurement basis choice. Furthermore, for the proposed scheme, we consider not only its asymptotic security case but also its composable security case, and the performance curves obtained in the latter are tighter than that achieved in the former. The proposed scheme aims to promote the practical process of underwater continuous variable quantum key distribution system and provide theoretical guidance for accurately evaluating the water channel parameters in underwater communication of global quantum communication networks.