System logs can record the system status and important events during system operation in detail. Detecting anomalies in the system logs is a common method for modern large-scale distributed systems. Yet threshold-based classification models used for anomaly detection output only two values: normal or abnormal, which lacks probability of estimating whether the prediction results are correct. In this paper, a statistical learning algorithm Venn-Abers predictor is adopted to evaluate the confidence of prediction results in the field of system log anomaly detection. It is able to calculate the probability distribution of labels for a set of samples and provide a quality assessment of predictive labels to some extent. Two Venn-Abers predictors LR-VA and SVM-VA have been implemented based on Logistic Regression and Support Vector Machine, respectively. Then, the differences among different algorithms are considered so as to build a multimodel fusion algorithm by Stacking. And then a Venn-Abers predictor based on the Stacking algorithm called Stacking-VA is implemented. The performances of four types of algorithms (unimodel, Venn-Abers predictor based on unimodel, multimodel, and Venn-Abers predictor based on multimodel) are compared in terms of validity and accuracy. Experiments are carried out on a log dataset of the Hadoop Distributed File System (HDFS). For the comparative experiments on unimodels, the results show that the validities of LR-VA and SVM-VA are better than those of the two corresponding underlying models. Compared with the underlying model, the accuracy of the SVM-VA predictor is better than that of LR-VA predictor, and more significantly, the recall rate increases from 81% to 94%. In the case of experiments on multiple models, the algorithm based on Stacking multimodel fusion is significantly superior to the underlying classifier. The average accuracy of Stacking-VA is larger than 0.95, which is more stable than the prediction results of LR-VA and SVM-VA. Experimental results show that the Venn-Abers predictor is a flexible tool that can make accurate and valid probability predictions in the field of system log anomaly detection.