CreateDialog[
Grid[{{B3, C1, C2, C3, C4, C5}, {C1,
B3C1C1 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C1C2 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C1C3 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C1C4 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C1C5 =
PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}]}, {C2,
B3C2C1 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C2C2 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C2C3 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C2C4 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C2C5 =
PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}]}, {C3,
B3C3C1 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C3C2 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C3C3 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C3C4 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C3C5 =
PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}]}, {C4,
B3C4C1 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C4C2 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C4C3 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C4C4 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C4C5 =
PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}]}, {C5,
B3C5C1 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C5C2 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C5C3 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C5C4 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}],
B3C5C5 = PopupMenu[1, {0, 1, 3, 5, 7, 9, 1/3, 1/5, 1/7, 1/9}]}},
Frame -> All]
ChoiceButtons[]]
CreateDialog[B3C2C3*B3C4C5*B3C1C2]

1.我想要在popupmenu里选完选项之后，把选出来的数再代入一个新的式子，但是带出来的是还是popupmenu。
2.为什么后面的程序不等前面的程序运行完就跳出下一个？

PopupMenu没有自动赋值机制（这个一般要配合Dynamic函数实现），具体请仔细阅读PopupMenu的帮助，不要想当然。
然后，关于没有等待的问题——这个在CreateDialog自带帮助的“可能存在的问题”里提及了——改用DialogInput就行了。