Micro-cantilever sensors are widely used to detect biomolecules, chemical gases, and ionic species. However, the theoretical descriptions and predictive modeling of these devices are not well developed, and lag behind advances in fabrication and applications. In this paper, we present a novel multiscale simulation framework for nanomechanical sensors. This framework, combining density functional theory (DFT) calculations and finite element method (FEM) analysis, is capable of analyzing molecular adsorption-induced deformation and stress fields in the sensors from the molecular scale to the device scale. Adsorption of alkanethiolate self-assembled monolayer (SAM) on the Au(111) surface of the micro-cantilever sensor is studied in detail to demonstrate the applicability of this framework. DFT calculations are employed to investigate the molecular adsorption-induced surface stress upon the gold surface. The 3D shell elements with initial stresses obtained from the DFT calculations serve as SAM domains in the adsorption layer, while FEM is employed to analyze the deformation and stress of the sensor devices. We find that the micro-cantilever tip deflection has a linear relationship with the coverage of the SAM domains. With full coverage, the tip deflection decreases as the molecular chain length increases. The multiscale simulation framework provides a quantitative analysis of the displacement and stress fields, and can be used to predict the response of nanomechanical sensors subjected to complex molecular adsorption.