Osteoporosis is an emerging health issue worldwide. Due to the decrease of bone mineral density and the deterioration of skeletal microarchitecture, osteoporosis could lead to increased bone fragility and higher fracture risk. Since lack of specific symptoms, novel serum proteomic indicators are urgently needed for the evaluation of osteoporosis. Microvesicles (MVs) are important messengers widely present in body fluids and have emerged as novel targets for the diagnosis of multiple diseases. In this study, MVs were successfully isolated from human serum and comprehensively characterized. Comparative proteomics analysis revealed differential MVs protein profiling in normal subjects, osteopenia patients, and osteoporosis patients. In total, about 200 proteins were identified and quantified from serum MVs, among which 19 proteins were upregulated (fold change >2) and five proteins were downregulated (fold change <0.5) in osteopenia group and osteoporosis group when compared with the normal group. Three protein candidates were selected for initial verification, including Vinculin, Filamin A, and Profilin 1. Profilin 1 was further pre-validated in an independent sample set, which could differentiate osteoporosis group from osteopenia group and normal group (p < 0.05). Our data collectively demonstrate that serum MVs proteome can be valuable indicators for the evaluation and diagnostics of bone loss disease.