Chronic kidney disease (CKD) is a global health problem with high morbidity and mortality rate, and it induces other diseases. Since there are no obvious symptoms during the early stages of CKD, patients often fail to notice the disease. Early detection of CKD enables patients to receive timely treatment to ameliorate the progression of this disease. Machine learning models can effectively aid clinicians achieve this goal due to their fast and accurate recognition performance. In this study, we propose a machine learning methodology for diagnosing CKD. The CKD data set was obtained from the University of California Irvine (UCI) machine learning repository, which has a large number of missing values. KNN imputation was used to fill in the missing values, which selects several complete samples with the most similar measurements to process the missing data for each incomplete sample. Missing values are usually seen in real-life medical situations because patients may miss some measurements for various reasons. After effectively filling out the incomplete data set, six machine learning algorithms (logistic regression, random forest, support vector machine, k-nearest neighbor, naive Bayes classifier and feed forward neural network) were used to establish models. Among these machine learning models, random forest achieved the best performance with 99.75% diagnosis accuracy. By analyzing the misjudgments generated by the established models, we proposed an integrated model that combines logistic regression and random forest by using perceptron, which could achieve an average accuracy of 99.83% after ten times of simulation. Hence, we speculated that this methodology could be applicable to more complicated clinical data for disease diagnosis.