Pore-scale modeling is becoming a hot topic in overall reservoir characterization process. It is an important approach for revealing the flow behaviors in porous media and exploring unknown flow patterns at pore scale. Over the past few decades, many reconstruction methods have been proposed, and among them the simulated annealing method (SAM) is extensively tested and easier to program. However, SAM is usually based on the two-point probability function or linear-path function, which fails to capture much more information on the multipoint connectivity of various shapes. For this reason, a new reconstruction method is proposed to reproduce the characteristics of a two-dimensional (2D) thin section based on the multipoint histogram. First, the two-point correlation coefficient matrix will be introduced to determine an optimal unit configuration of a multipoint histogram. Second, five different types of seven-point unit configurations will be used to test the unit configuration selection algorithm. Third, the multipoint histogram technology is used for generating the porous space reconstruction based on the prior unit configuration with a different calculation of the objective function. Finally, the spatial connectivity, patterns reproduction, the local percolation theory (LPT), and hydraulic connectivity are used to compare with those of the reference models. The results show that the multipoint histogram technology can produce better multipoint connectivity information than SAM. The reconstructed system matches the training image very well, which reveals that the reconstruction captures the geometry and topology information of the training image, for instance, the shape and distribution of pore space. The seven-point unit configuration is enough to get the spatial characters of the training image. The quality of pattern reproduction of the reconstruction is assessed by computing the multipoint histogram, and the similarity is around 97.3%. Based on the LPT analysis, the multipoint histogram can describe the anticipated patterns of geological heterogeneities and reproduce the connectivity of pore media with a high degree of accuracy. The two-point correlation coefficient matrix and a new construction theory are proposed. The new construction theory provides a stable theory and technology guidance for the study of pore space development and multiphase fluid flow rule in the digital rock.