We present a new methodology to derive the positions of the Sgr B molecular clouds (MCs) along the line of sight, as an application study of the Galactic center diffuse X-rays (GCDX). The GCDX is composed of hot plasma emission of about 7 keV and 1 keV temperatures, and non-thermal continuum emission including the 6.4 keV line from neutral irons. The former, the Galactic center plasma emission (GCPE), is uniformly distributed over 1 degree in longitude, while the latter is clumpy emission produced by Thomson scattering and fluorescence from MCs irradiated by external X-rays (the X-ray reflection nebula emission: XRNE). We examined the Suzaku X-ray spectra of the GCPE and XRNE near to the Sgr B MC complex, and found that the spectra suffer from two different absorptions of N_H (Abs1) >= 1023 H cm-2 and N_H (Abs2) 6*1022 H cm-2. Abs1 is proportional to the 6.4 keV-line flux, and hence is due to the MCs, while Abs2 is typical of interstellar absorption toward the Galactic center. Assuming that the GCPE plasma is spherically-extended around Sgr A* with a uniform density and the same angular distribution of the two temperature components, we quantitatively estimated the line-of-sight positions of the MCs from the flux ratio the GCPE spectrum suffered by Abs1 and that with no Abs1. The results suggest that the Sgr B MCs are located at the near side of Sgr A* in the GCPE.