In radiobiology, in vitro irradiation experiments on cells are often conducted to investigate the relationship between radiation dose and biological effects, where the phenotypic indicators of cells in culture are generally measured with macroscopic dosimetric indicators of the absorbed dose. The intracellular transport behavior of low-energy electrons are of particular importance. Considering the states of cells in culture, two-dimensional monolayer mesh-type cell population models were constructed in this work based on two human mesh-type cell models to evaluate the microdosimetric distribution of monoenergetic electrons with two energy levels in the cell population. Two-dimensional monolayer mesh-type and equivalent-volume concentric sphere cell population models of two cell lines, i.e., BEAS-2B and FHs74Int, with different cell numbers and shapes were constructed. Monte Carlo toolkit, GATE, was used as the simulation platform. The impacts of different deposition doses from the 100 keV and 200 keV monoenergetic electron beams on the average specific energy z‾ of the nucleus and cytoplasm, the specific energy frequency function f(z,D), and their relative standard deviation σz/z‾ were assessed. Under the same irradiation conditions, the mesh-type and equivalent-volume sphere cell population models showed small differences in f(z,D), whereas the z‾ of the nucleus and cytoplasm differed significantly. As the cumulative absorbed dose reached the mGy level under the irradiation of the monoenergetic electron beam with an initial energy of 100 keV, the nucleus z‾ of the FHs74Int circular mesh-type population model with 848 cells was 19.88 mGy, whereas the nucleus z‾ of the concentric sphere cell population model was 23.96 mGy. The lower dose (∼mGy level) under the same geometry resulted in a more pronounced uncertainty in the absorbed dose value. Specifically, take the FHs74Int quadrate mesh-type population model with 484 cells as an example, the σz/z‾ were 3.61% and 23.35%, respectively, at the ∼Gy and ∼mGy levels under electrons with the initial energy of 200 keV. In addition, the volume and shape of the cell population impact the specific energy distribution. Through the constructed two-dimensional monolayer mesh-type cell population model, this work quantitatively demonstrates that the dose distribution within subcellular regions under low-energy electron irradiation for low-dose level is significantly affected by the cell volume and shape. This study provides a viable means of simulating and quantifying the energy deposition distribution of radiation within the culture dish based on radiobiological cell irradiation scenarios, which can provide method and data support to build biophysical models.