In the era of the Fourth Industrial Revolution, the increasing demand for data collection and sharing for analysis purposes has raised concerns regarding privacy violations. Protecting individual privacy during the collection and dissemination of sensitive information has emerged as a critical concern. In this paper, we propose a privacy-preserving framework for collecting users’ medical microdata, utilizing geo-indistinguishability (Geo-I), a concept based on well-known differential privacy. We adapt Geo-I, originally designed for protecting location information privacy, to collect medical microdata while minimizing the reduction in data utility. To mitigate the reduction in data utility caused by the perturbation mechanism of Geo-I, we propose a novel data perturbation technique that utilizes the prior distribution information of the data being collected. The proposed framework enables the collection of perturbed microdata with a distribution similar to that of the original dataset, even in scenarios that demand high levels of privacy protection, typically requiring significant perturbations to the original data. We evaluate the performance of our proposed algorithms using real-world data and demonstrate that our approach significantly outperforms existing methods, ensuring user privacy while preserving data utility in medical data collection.