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Boron doped hydrogenated nanocrystalline silicon (nc-Si:H) thin films are deposited using layer-by-layer technique in radio frequency (RF) plasma enhance chemical vapor deposition system. Studies about the influence of gas pressure, RF power density and buffer layer in i/p interface on the microstructure and electrical properties of Boron doped nc-Si:H thin films have been carried out. The experimental results have shown that a), as the gas pressure decreases, the grain size of nc-Si:H thin film increases, while its conductivity turns small, and the thin films transform into amorphous silicon when the gas pressure decreases to 100 Pa; b), the microstructure of nc-Si:H thin films evolves to more ordered when the power density was enhanced from 280 mW/cm2 to 560 mW/cm2, and the grain size changes to be larger; c), the thickness of i/p buffer has large effect on the microstructure of Si:H thin films, when the deposition time of buffer layer increases from 0 min to 10 min, the Si:H thin films changes from amorphous to nanocrystalline, however the optimal time is about 2 min. When the boron doped nc-Si:H thin films are applied as the window layer of n-i-p flexible amorphous silicon solar cells, comparing with p type a-SiC:H window layer, the performance of solar cells have been largely improved.