His mother has told him many times,but it did not help

完全可以，英语是灵活的，你甚至可以用 His mother has told him many times which did not help.

看来你确实很又学习语言的天赋~

相信我，我搞专业的~

it是最自然的，如果说用that不是不可以的，只是觉得有些怪怪的

His mother has told him nay times (before), but it (that, telling him alone) did not help (at all). 说明这个孩子太顽固，母亲单靠提醒是改不掉他的坏习惯的，比如衣服不能在地上乱扔。

觉得不太适合
因为前面没有说到具体的事情，如果说told一件具体的事，用that比较好

不行,用 that的话要放整句话之前,比如:tnat his mother told him not to throw about didnot help a little. 你的是简单句,用that是名词从句.

可以用that
但是that和it一样，只能表示“他妈妈告诉他很多次”这个内容

可以，英语注重的是结构。