Aiming at the security analysis problem of KATAN48 algorithm, a conditional differential cryptanalysis method of KATAN48 algorithm based on neural distinguishers was proposed. First, the basic principle of multiple output differences neural distinguishers was studied and applied to KATAN48 algorithm. According to the data format of KATAN48 algorithm, the input format and hyperparameters of the deep residual neural network were adjusted. Then, the Mixed-Integer Linear Programming (MILP) model of KATAN48 algorithm was established to search the prepended differential paths and the corresponding constraint conditions. At last, using the multiple output differences neural distinguishers, at most 80-round of the practical key recovery attack results of KATAN48 algorithm were given. Experimental results show that in the single key setting, the number of practical attack rounds of KATAN48 algorithm is increased by 10 rounds, the number of recoverable key bits of KATAN48 algorithm is increased by 22 bit and the data complexity and time complexity of KATAN48 algorithm are reduced from 234 and 234 to 216.39 and 219.68 respectively. Compared to the previous practical attack at the single-key setting, the proposed method can effectively increase the number of attack rounds and recoverable key bits, and reduces the computational complexity of attack.