你的这个句子书写有误。应为：

What difference did it make that she was beautiful?

为了理解方便，我们把该句变成陈述句：

It made much difference that she was beautiful.

【结构分析】

1. make difference：是个习语。意为“关系重大；有所作为；造成差别；有不同之处”。

2. It是形式主语。

3. that she was beautiful：是真实主语。

【注意】不过，我认为这个句子在逻辑上有误。就是说，that she was beautiful——这个that从句陈述了一种事实，应改为带有疑问的名词性从句或者条件句更符合逻辑。例如：

It made much difference whether she was beautiful. 她是否长得漂亮情况有很大的区别。

It made much difference if she was beautiful. 她如果长得漂亮的话，情况就有很大区别。

What difference did it make whether she was beautiful? 她长得是否漂亮有什么不同吗？

What difference did it make if she was beautiful? 如果她漂亮的话，会有什么不同呢？