Aiming to address the issue of assessing the effectiveness of target damage in air defense interception under projectile and target intersection, this paper proposes a novel target damage effectiveness assessment mathematical calculation method using an adaptive fuzzy neural network. The design and calculation methods introduce the target cabin’s damage weight factor, the dispersion error and coverage density and fire density of warhead fragment, and the ratio of the number of warhead fragments to the cross-sectional area of the target as the primary damage factors, and we establish a new model for calculating the target damage efficiency using Takagi-Sugeno adaptive fuzzy neural network with the multiple damage factors. In the designed model, we take the characteristic parameters of warhead fragments formed by the projectile explosion as the sample data and learn the mapping relationship between damage factors and damage effect expressed by the system of fuzzy rule. Combined with the vulnerability weight and damage factors of the target, the fuzzy rule system is applied to predict and calculate the damage probability and damage effectiveness. In addition, we use shot-line technology to set up the intersection criterion between warhead fragments and target, analyze the coordinate relationship of the projectile explosion relative to the target based on the ground coordinate system, and derive the distribution density function of warhead fragment and research a calculation model for target damage probability with multiple vulnerable cabins. Finally, we use the established model to train, test, and calculate the data from the actual projectile and target intersection damage test and present the comparison results to other damage calculation methods. By calculation and comparative analysis, the results show the smaller the distance between projectile and target, as well as the smaller the average intersection angle, and the larger the weight coefficient of the warhead fragment covering the target cabin, the total target damage probability increases obviously. In the two experimental calculations, the target cabin with the largest weight coefficient was considered, and compared with the existing literature, the damage probability of the proposed calculation method was increased by 9.13% and 10.93%, respectively, and it is clear that the proposed target damage assessment method can effectively reflect the real target damage effectiveness in the state of projectile and target intersection.