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With the rapid development of information technology and the spread of Corona Virus Disease 2019 (COVID-19), the government and urban managers are looking for ways to use technology to make the city smarter and safer. Intelligent transportation can play a very important role in the joint prevention. This work expects to explore the building information modeling (BIM) big data (BD) processing method of digital twins (DTs) of Smart City, thus speeding up the construction of Smart City and improve the accuracy of data processing. During construction, DTs build the same digital copy of the smart city. On this basis, BIM designs the building's keel and structure, optimizing various resources and configurations of the building. Regarding the fast data growth in smart cities, a complex data fusion and efficient learning algorithm, namely Multi-Graphics Processing Unit (GPU), is proposed to process the multi-dimensional and complex BD based on the compositive rough set model. The Bayesian network solves the multi-label classification. Each label is regarded as a Bayesian network node. Then, the structural learning approach is adopted to learn the label Bayesian network's structure from data. On the P53-old and the P53-new datasets, the running time of Multi-GPU decreases as the number of GPUs increases, approaching the ideal linear speedup ratio. With the continuous increase of K value, the deterministic information input into the tag BN will be reduced, thus reducing the classification accuracy. When K = 3, MLBN can provide the best data analysis performance. On genbase dataset, the accuracy of MLBN is 0.982 +/- 0.013. Through experiments, the BIM BD processing algorithm based on Bayesian Network Structural Learning (BNSL) helps decision-makers use complex data in smart cities efficiently.