Cosmic ray muon tomography is a promising method for the non-invasive inspection of shipping containers and trucks. It leverages the highly penetrating cosmic muons and their interactions with various materials to generate three-dimensional images of large and dense objects, such as inter-modal shipping containers, which are typically opaque to conventional X-ray radiography techniques. One of the key tasks of customs and border security is verifying shipping container declarations to prevent illegal trafficking, and muon tomography offers a viable solution for this purpose. Common imaging methods using muons rely on data analysis of either muon scattering or absorption-transmission. We have designed a compact muon tomography system with dimensions of 3 × 3 × 3 m3, consisting of 2-D position-sensitive detectors. These detectors include plastic scintillators, wavelength-shifting (WLS) fibers, and SiPMs. Through light transport modeling with GEANT4, we demonstrated that the proposed detector design—featuring 1 m × 1 m scintillator plates with 2 mm2 square-shaped WLS fibers—can achieve a spatial resolution of approximately 0.7-1.0 mm. Through Monte Carlo simulations, we show that a combined analysis of muon scattering and absorption data enables prompt identification of cargo materials. In a smuggling scenario where tobacco is declared as paper towel rolls, the combined analysis accurately distinguishes between tobacco and paper towel rolls with 3 σ confidence at 1 mm spatial resolution, within a short scanning time of 40 seconds for the entire 20-foot shipping container.