We present the result of the in-flight calibration of the effective area of the Soft X-ray Spectrometer (SXS) onboard the Hitomi X-ray satellite using an observation of the Crab nebula. We corrected for the artifacts when observing high count rate sources with the X-ray microcalorimeter. We then constructed a spectrum in the 0.5-20 keV band, which we modeled with a single power-law continuum attenuated by an interstellar extinction. We evaluated the systematic uncertainty upon the spectral parameters by various calibration items. In the 2-12 keV band, the SXS result is consistent with the literature values in flux (2.20 $pm$ 0.08) $times$10$^{-8}$ erg s$^{-1}$ cm$^{-2}$ with a 1$sigma$ statistical uncertainty) but is softer in the power-law index (2.19 $pm$ 0.11). The discrepancy is attributable to the systematic uncertainty of about $+$6/$-$7% and $+$2/$-$5% respectively for the flux and the power-law index. The softer spectrum is affected primarily by the systematic uncertainty of the Dewar gate valve transmission and the event screening.
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