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With the growing demand for smart, secure, and intelligent solutions, Industry 4.0 has emerged as the future of various applications. One of the primary sectors that are becoming more vulnerable to security assaults like ransomware is the healthcare sector. Researchers have proposed various mechanisms in smart and secure health care systems with this vision in mind. Existing systems are vulnerable to security attacks on medical data. It is required to build a real-time diagnosis device using a cyber-physical system with blockchain technology in a considerable manner. The proposed work’s main purpose is to build secure, real-time preservation and tamper-proof control of medical data. In this work, the Bayesian grey filter-based convolution neural network (BGF-CNN) approach is used to enhance accuracy and reduce time complexity and overhead. Additionally, PSO and GWO optimization techniques are used to improve network performance. As an outcome of the proposed work, the privacy preservation of medical data is improved with a high accuracy rate by a blockchain-based cyber-physical system using a deep neural network (BGF Blockchain). To summarize, the proposed system helps in the privacy preservation of medical data along with a reduction in communication overhead using the Bayesian Grey Filter–CNN.