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In this study, a nanocrystalline diamond thin film is applied on a quartz substrate using hot filament chemical vapor deposition (HFCVD) with a mixture of methane and hydrogen gas. Taguchi’s method with L9 (34) orthogonal array is used to design the experimental parameters. Moreover, the effects of the CH4/H2 ratio, the chamber pressure, the substrate temperature, and total gas flow rate on the qualities of the nanocrystalline diamond film are discussed. Film growth rate, surface roughness and transmittance in the visible waveband are considered quality characteristics. With signal-to-noise ratio and the average value of the quality characteristics, optimal parameters can be found. In the analysis of variance and F test, an optimal quality characteristic can be predicted after eliminating factors with less influence. Before the diamond deposition, electrophoresis and Polyetherimide (PEI) adhesion methods as pretreatment on the quartz substrate are compared and discussed for their effects on nucleation density. The optimal parameters obtained in this study are 12% CH4/H2, the chamber pressure of 10 Torr, 600 o C substrate temperature, and total gas flow rate of 100 sccm. With these parameters, the transmittance in the visible waveband of a diamond film on quartz substrate can reach to 60%.