As computer technology continues to advance, more and more people are using databases, leading to variations in data backup and transfer between databases. This paper proposes a small sample inter-database discrepancy data elimination method based on cloud computing architecture as a way to solve the problem of data synchronization discrepancy between different databases. The semantic features of the data in the database are represented in the form of a directed graph, and the semantic Gaussian marginalized data fusion system is constructed by combining the rectangular window function of Gaussian marginalization to realize the fusion filtering processing of discrepant data. Then, the particle swarm discriminant tree algorithm is used to extract the features of the difference data between the small sample databases, and the KL transform is used to compress the difference data to improve its confidence level. The rough weighted average single dependency method is introduced to detect and identify the difference data between small sample databases and combined with the artificial intelligence algorithm to construct the principal component feature set of the difference data in the small sample databases, thus realizing the elimination of the difference data between small sample databases. When the proportion of difference data is increased from 0.05% to 1.00%, the leakage alarm rate and false alarm rate of this paper’s method for the difference data between small sample databases are 0.113% and 0.099%, respectively. When eliminating the inter-database discrepancy data, its time consumption is between 0.06μs and 0.3μs, and the average value of the removal rate of discrepancy data can reach 95.54%. Small sample databases that utilize cloud computing technology can utilize a variety of differential data elimination algorithms to ensure high-quality migration and synchronized backup of inter-database data.