To predict the shear stress of magnetorheological fluids (MRFs) under magnetic field and shear flows, a meso-microscale shear model is proposed based on the entire course of particle aggregates and chains. For this purpose, a systematic study on the microstructure evolution and rheological properties of MRFs is conducted by using molecular dynamics simulations. An efficient chain identification technique is introduced to count the number of particle chains within the suspension system. From the perspective of particle-level simulations, the microstructured behavior of MRFs involving particle aggregation and internal structure evolution of magnetorheological suspensions are addressed. Shear properties of MRFs derived by the proposed model are studied, and model verification by comparison with previous experimental data and predictions of the existing structural viscosity model is included as well. It is revealed that the proposed meso-microscale shear model exhibits satisfactory accuracy and efficiency for describing the rheological properties of MRFs. Besides, the critical factors linked with rheological properties of MRFs such as magnetic field strength, particle volume fraction and shear rate, are analyzed, further demonstrating the applicability of the proposed model in design and optimization of MRFs.