Since the actual chromatogram data of the water-flooded layer have characteristics of multiple dimension, complexity and noise, it is difficult to accurately identify and appraise the water-flooded layer in the oil and gas reservoirs. Therefore, this article proposes a recognition modeling approach based on the intelligent ensemble classifier, integrated model-free Bayesian classifier, the AdaBoost algorithm and the support vector machine algorithm. The effective chromatogram characteristic information can be obtained using the curve fitting method. In order to transform the sparse classification problem into a general classification problem, the synthetic minority over-sampling technique algorithm is used to process an unbalanced training sample as a general training sample. Moreover, the model-free Bayesian classifier, AdaBoost and support vector machine algorithms are used as the base classifiers to train the ensemble classification model. Compared to the traditional single classification approach, the robustness and the effectiveness of the ensemble classifier model are validated through the standard data source from the UCI (University of California at Irvine) repository. Finally, the proposed model is applied in the identification and appraisal of the water-flooded layers in a complex oil and gas recognition system. The chromatogram characteristic information and the prediction results are obtained to provide more reliable water-flooded layer information, guide the process of reservoir exploration and improve the oil development efficiency.