The microscopic pore structure controls the fluid seepage characteristics, which in turn affect the final recovery of the reservoir. The pore structures of different reservoirs vary greatly; therefore, the scientific classification of microscopic pore structures is the prerequisite for enhancing the overall oil recovery. For the low permeability conglomerate reservoir in Mahu Sag, due to the differences in the sedimentary environment and late diagenesis, various reservoir types have developed in different regions, so it is very difficult to develop the reservoir using an integrated method. To effectively solve the problem of microscopic pore structure classification, the low permeability conglomerate of the Baikouquan Formation in Well Block Ma18, Well Block Ma131, and Well Block Aihu2 are selected as the research objects. The CTS, HPMI, CMI, NMR, and digital cores are used to systematically analyze the reservoir micro pore structure characteristics, identify the differences between different reservoir types, and optimize the corresponding micro pore structure characteristic parameters for reservoir classification. The results show that the pore types of the low permeability conglomerate reservoir in the Baikouquan Formation of the Mahu Sag are mainly intragranular dissolved pores and residual intergranular pores, accounting for 93.54%, microfractures and shrinkage pores that are locally developed, accounting for 5.63%, and other pore types that are less developed, accounting for only 0.83%. On the basis of clear pore types, the conglomerate reservoir of the Baikouquan Formation is divided into four types based on the physical properties and microscopic pore structure parameters. Different reservoir types have good matching relationships with lithologies. Sandy-grain-supported conglomerate, gravelly coarse sandstone, sandy-gravelly matrix-supported conglomerate, and argillaceous-supported conglomerate correspond to type I, II, III, and IV reservoirs, respectively. From type I to type IV, the corresponding microscopic pore structure parameters show regular change characteristics, among which, porosity and permeability gradually decrease, displacement pressure and median pressure increase, maximum pore throat radius, median radius, and average capillary radius decrease, and pore structure becomes worse overall. Apparently, determining the reservoir type, clarifying its fluid migration rule, and formulating a reasonable development plan can substantially enhance the oil recovery rate of low permeability conglomerate reservoirs.