Nonlocal effects are widely identified in micro/nano systems and have been studied extensively in recent decades. Nevertheless, existing studies mostly focus on the modeling of homogeneous nonlocal systems and as a result, cannot model micro/nanostructures with heterogeneously distributed nonlocal effects. This study introduces a reduced-order nonlocal Timoshenko beam model that facilitates precise modeling of micro-elastic beams with layer-wise heterogeneous nonlocal effects. First, a fully-resolved two-dimensional (2D) plane-strain fractional-order nonlocal elastic framework is developed to provide reference solutions for 2D nonlocal beam problems. Building upon this general nonlocal elasticity theory, an equivalent one-dimensional (1D) nonlocal Timoshenko model is then developed. The layer-wise heterogeneous nonlocal information is captured by using distributed-order (DO) operators, and the impacts arising from the nonlocal heterogeneity are further characterized by introducing two auxiliary parameters. Both 1D and 2D approaches are applied to simulate the mechanical responses of nonlocal beams. Direct comparisons of numerical simulations produced by either the 1D or the fully-resolved 2D model confirm that the DO Timoshenko beam formulation (together with the two auxiliary parameters) can capture not only the overall beam deflection but also the additional shear effect induced by the heterogeneous nonlocality. Computational cost assessment also indicates the proposed approach’s superior performance. The proposed DO Timoshenko model enables model-order reduction without compromising the heterogeneous nonlocal description of the material hence leading to an efficient and accurate reduced-order nonlocal modeling approach that addresses the limitations of prior nonlocal microstructural theories and extends applicability to a broader range of heterogeneous nano/microstructures.