I don't really get the question so I hope this is what you wanted. If you include a full document (such that we copy paste and see the problem on our systems) things are much more easier.
Here, you can change the default setting within a scope but your block style had a node distance which was resetting every time it is issued. I've made it 2mm such that we can see the difference easier.
\documentclass[tikz]{standalone}\usetikzlibrary{arrows,shapes.geometric,positioning}\begin{document}\begin{tikzpicture}[decision/.style={diamond, draw, text width=4.5em, text badly centered, node distance=3.5cm, inner sep=0pt}, block/.style ={rectangle, draw, text width=6em, text centered, rounded corners, minimum height=4em, minimum height=2em}, cloud/.style ={draw, ellipse, minimum height=2em}, line/.style ={draw,-latex'}, node distance = 1cm, auto] \node [block] (1st) {1st}; \node [block, right= of 1st] (2nd1) {2nd1};\begin{scope}[node distance=2mm and 10mm]%Here we change it for everything inside this scope \node [block, above= of 2nd1] (2nd2) {2nd2}; \node [block, below= of 2nd1] (2nd3) {2nd3}; \node [block, right= of 2nd1] (3rd1) {3rd1}; \node [block, above= of 3rd1] (3rd2) {3rd2}; \node [block, above= of 3rd2] (3rd3) {3rd3};\end{scope} \node [block, below= of 3rd1] (3rd4) {3rd4}; \node [block, below= of 3rd4] (3rd5) {3rd5}; \path [line] (1st) -- (2nd1); \path [line] (2nd1) -- (2nd2); \path [line] (2nd1) -- (2nd3); \path [line] (2nd2) -- (3rd3); \path [line] (2nd1) -- (3rd1); \path [line] (1st) -- (2nd1);\end{tikzpicture}\end{document}