Automatic themes-based classification of Quran verses is the process of classifying verses to predefined categorizes or themes. It is an essential task for all Muslims and people interested in studying the Quran. Quran themes-based classification could be used in many natural language processing (NLP) fields such as search engines, data mining, question-answering systems, and information retrieval applications. This paper presents an ensemble multi-label classification model that automatically identifies and classifies the Quran verses based on themes/topics. The model is composed of four phases: pre-processing, data vectorization, binary relevance classifier, and voting module. Firstly, the verses of the second chapter of the Quran (Al-Baqarah) are tokenized and normalized. Then, the topics of these verses are manually labeled based on "Mushaf Al-Tajweed" classification. Secondly, verses are converted into features' vectors using term frequency-inverse document frequency (TF-IDF) and word2vec techniques. Word2vec is used to consider the semantic meaning of Quranic words and to improve performance. Also, they are trained on a collected classic Arabic corpus of 200 million words. Then, the binary relevance multi-label classification technique is applied using three different classifiers: logistic regression, support vector machine, and random forest, which categorize verses into 393 topics/tags. Finally, the voting module is applied by picking the tags with the maximum prediction probability among the three classifiers. The results of the three classifiers and the ensemble model are compared against "Mushaf Al-Tajweed." The ensemble model outperforms the three classifiers. Its average hamming loss, recall, precision, and F1-Score are 0.224, 81%, 75%, and 77%, respectively.