The sudden resignation of core employees often brings losses to companies in various aspects. Traditional employee turnover theory cannot analyze the unbalanced data of employees comprehensively, which leads the company to make wrong decisions. In the face the classification of unbalanced data, the traditional Support Vector Machine (SVM) suffers from insufficient decision plane offset and unbalanced support vector distribution, for which the Synthetic Minority Oversampling Technique (SMOTE) is introduced to improve the balance of generated data. Further, the Fuzzy C-mean (FCM) clustering is improved and combined with the SMOTE (IFCM-SMOTE-SVM) to new synthesized samples with higher accuracy, solving the drawback that the separation data synthesized by SMOTE is too random and easy to generate noisy data. The kernel function is combined with IFCM-SMOTE-SVM and transformed to a high-dimensional space for clustering sampling and classification, and the kernel space-based classification algorithm (KS-IFCM-SMOTE-SVM) is proposed, which improves the effectiveness of the generated data on SVM classification results. Finally, the generalization ability of KS-IFCM-SMOTE-SVM for different types of enterprise data is experimentally demonstrated, and it is verified that the proposed algorithm has stable and accurate performance. This study introduces the SMOTE and FCM clustering, and improves the SVM by combining the data transformation in the kernel space to achieve accurate classification of unbalanced data of employees, which helps enterprises to predict whether employees have the tendency to leave in advance.