To realize metrology of the nanometer thin film thickness with high accuracy, a series of the nanometer film thickness standard samples with single layer is developed which could be measured by contact instruments such as stylus contact surface step profiler and scanning probe microscopy. The measurement and calculation method of grazing incidence X-ray reflectometry (GIXRR) for film thickness are studied. The formula of linear fitting method based on the periodic Kiessig fringes for thickness measurement is presented. A tracing approach of film thickness measurement, which is traceable to the atomic lattice of monocrystalline silicon and national angle standard, is proposed, and a new optics calibration method is presented which can measure angular misalignment of GIXRR apparatus. The relative expanded uncertainty of the nanofilm thickness H measurement is U=0.3 nm+1.5%H with coverage factor k=2.