The development and distribution of geologically complicated fault structure have the characteristics of uncertainty, randomness, ambiguity, and variability. Therefore, the prediction of complicated fault structures is a typical nonlinear problem. Neither fuzzy logic method nor artificial neural network alone can solve this problem well because the fuzzy method is generally not easy to realize adaptive learning function, and the neural network method is not suitable for describing sedimentary microfacies or geophysical facies. Therefore, taking the marginal subsags in the Jiyang Depression, Eastern China, as a study case, this paper uses the method of combining artificial neural network and fuzzy logic to study geologically complicated fault structure prediction model. This paper expounds on the research status and significance of geologically complicated fault structure prediction model, elaborates the development background, current status, and future challenges of artificial neural networks and fuzzy logic, introduces the method and principle of fuzzy neural network structure and fuzzy logic analysis algorithm, conducts prediction model design and implementation based on fuzzy neural network, proposes the learning algorithm of fuzzy neural network, analyzes the programming realization of fuzzy neural network, constructs complicated fault structure prediction model based on the artificial neural network and fuzzy logic, performs the fuzzy logic system selection of complicated fault structure prediction model, carries out the artificial neural network structure design of complicated fault structure prediction model, compares the prediction effects of the geologically complicated fault structure model based on artificial neural networks and fuzzy logic, and finally discusses the system design and optimization of the prediction model for geologically complicated fault structures. The study results show that the fuzzy neural network fully integrates the advantages of artificial neural network and fuzzy logic system; based on the clear physical background of fuzzy logic system, it effectively integrates powerful knowledge expression ability and fuzzy reasoning ability into the network knowledge structure of neural network, which greatly improves the prediction accuracy of geologically complicated fault structure.