The unknown nature and complexity of non-uniform formations cause new difficulties and challenges to the accurate detection of electrical instruments in shallow formations. The micro-cylindrically focused logging tool (MCFL) can provide three original measurement curves, RB0, RB1, and RB2, with different detection depths, which reflect the flushing zone resistivity, mudcake resistivity, and mudcake thickness. In this study, the finite element method was used to model and analyze the micro-cylindrically focused logging tool tool in a three-dimensional non-uniform medium model. By converting the partial differential equation into a generalized polar problem, the logging response characteristics of the micro-cylindrically focused logging tool tool at different detection depths and ranges, mudcake thicknesses, flush zones, and mudcake resistivity contrasts were investigated. Inverse processing of the micro-cylindrically focused logging tool data using the least-squares method was used to obtain the flush zone resistivity, mudcake resistivity, and mudcake thickness, based on which the micropotential and microgradient curves were synthesized. In addition, a digital focusing method was proposed to improve the focusing accuracy and flexibility of the instrument, enhancing the performance of the micro-cylindrically focused logging tool. The optimized design of the focusing method significantly improved the detection performance of the pole plate. This plays an important role in the evaluation of thin layers and oil-water reservoirs.