查了好多资料，差点就动手翻Java源码了，最后结合一篇文章（忘记出处了），想到了输出流会阻塞进程执行。 Java进程执行有一个输入流，两个输出流(相对于外部程序)。当两个输出流有内容输出，而Java执行程序没有及时清空输出流时就会阻塞进程。
现贴出代码，希望能帮助到有需要的同行：

复制代码 代码如下:/**
* pdf转swf函数
* @param path 输入输出文件路径
* @param inputFileName 输入文件名
* @param outputFileName 输出文件名
* @return File 生成的swf文件
*/
private static File toSwf(String sourceFile, String destFile, String command) {
long beginTime = System.nanoTime();
Runtime rt = Runtime.getRuntime();
try {
Process process = rt.exec(command);

final InputStream isNormal = process.getInputStream();
new Thread(new Runnable() {
public void run() {
BufferedReader br = new BufferedReader(new InputStreamReader(isNormal));
StringBuilder buf = new StringBuilder();
String line = null;
try {
while((line = br.readLine()) != null){
buf.append(line + "\n");
}
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("输出结果为：" + buf);
}
}).start(); // 启动单独的线程来清空process.getInputStream()的缓冲区

InputStream isError = process.getErrorStream();
BufferedReader br2 = new BufferedReader(new InputStreamReader(isError));
StringBuilder buf = new StringBuilder();
String line = null;
while((line = br2.readLine()) != null){
buf.append(line + "\n");
}
System.out.println("错误输出结果为：" + buf);

try {
process.waitFor();
} catch (InterruptedException e) {
e.printStackTrace();
}

} catch (IOException e) {
e.printStackTrace();
}
long endTime = System.nanoTime();
System.out.println("转swf耗时: " + (endTime - beginTime) / 1000000000 + " 秒 " + sourceFile);
return new File(destFile);
}