A
本句包含了强调句型It's.that.
该句主干
It was in that small village that he spent his childhood
（去除强调即为 In that small village he spent his childhood）一个普通正确句子
现被强调部分that small village后面有一个定语从句 _____ was destoryed by the flood ,由于该定语从句缺少了主语,故填which,而不是where.
相信你能理解赞同吧!