The procedures of sample preparation for isotopic determination of boron in clay sediments is very cumbersome, by far, there haven’t been relevant reports on that. In order to establish an effective method for sample preparation, a series of experiments were carried out. In this paper, boron in clay sediments was extracted with HCl solution and purified by two-step ion exchange method. Extracted HCl solution should be adjusted to alkalescency before passing through the Amberlite IRA 743 resin column due to the fact that Amberlite IRA 743 resin absorbs boron only from alkalescent solution. However, a mass of hydroxides of Al and Fe will be precipitated when the extracted HCl solution becomes alkalescent. Hydroxides of Al and Fe have a strong adsorption capacity for boron, which can cause boron isotope fractionation. To treat precipitated hydroxides of Al and Fe, four procedures, namely direct ion exchange (DRIE), decationizing ion exchange (DCIE), once sedimentation ion exchange (OSIE) and repeated sedimentation ion exchange (RSIE) were used and assessed. The influences of the four procedures on separation and extraction and isotopic composition of boron in experimental solutions and clay sediments were also discussed. According to the results, the DRIE, DCIE and OSIE are improper. The result of sample determination indicates that when extracting boron via RSIE, with the increase of precipitation times, there’s an obvious decrease in boron content in the precipitated hydroxides while a sharp increase in recovery of boron and it is favorable for weakening the influence of boron isotope fractionation. But the process of RSIE is time consuming and it may introduce boron. It needs further research to establish a more effective sample preparation method for isotopic determination of boron in clay sediments.