Using purely electrical methods to manipulate magnetic property poses a significant obstacle in the development of advanced information technology. Multiferroic materials, distinguished by their magnetoelectric (ME) effect, offer a promising way to overcome this challenge by enabling the electric control of magnetic ordering or magnetization. Here, we have synthesized Cu3Mo2O9 single crystals and investigated the anisotropic ME effect within the quasi-one-dimensional spin system. The simultaneous occurrence of ferroelectric (FE) polarization and dielectric anomaly at the Néel temperature (TN) of ∼7.9 K suggests the presence of spin-driven FE property in Cu3Mo2O9. The phase transition temperatures undergo a shift toward lower values for H//c and remain constant for H//a and H//b, indicating anisotropic ME effect. The ME effect demonstrates nonlinear behavior as the magnetic field increases. Near a critical point (T = 7 K and μ0H = 5.6 T), a giant magnetodielectric coupling parameter reaching 374% is observed for H//c, which can be ascribed to the strong spin–phonon coupling and the magnetic field induced change of FE polarization. In the context of charge redistribution without magnetic superlattice, the FE property is analyzed. Moreover, remarkable magnetic control of FE polarization and electric control of magnetization are obtained. The temporal evolution of both polarization and magnetization indicates the stable ME mutual control, suggesting potential applications of Cu3Mo2O9 as a promising multiferroic material.