In general they can be very different. For example take the subscheme $Y$ of $\mathbb{A}^2$ given by the ideal $(x^2,y)$. Here the blow up is covered by the two open subsets
$$U = \mbox{Spec} k[x, y][t]/(y − x^2t),\qquad V = \mbox{Spec} k[x, y][s]/(ys − x^2)$$
In particular the blow up of $Y$ is singular, whereas the blow-up of $\mathbb{A}^2$ at a point is not.
In general, even if you assume that both blow-ups are smooth, all sorts of things can happen depending on how complicated the ideal sheaf is. For example the blow-ups can have a different number of exceptional divisors and not even be related by a finite map. Even worse, every birational morphism $X'\to X$ is the blow-up of $X$ along some ideal sheaf.
On the other hand I guess it is true is that there will be some third blow-up $Bl_{Z}(X)$, which dominates both $Bl_{Y}(X)$ and $Bl_{Y_{red}}(X)$.