Apache FOP在设计上是线程安全的。但是，首先需要确保所有的依赖类库也是线程安全的。建议使用线程池来同时处理多个文档。下面是一个使用线程池的示例代码：

ExecutorService pool = Executors.newFixedThreadPool(10);

for (int i = 0; i < numDocuments; i++) {
    pool.submit(new Runnable() {
        public void run() {
            try {
                FOUserAgent userAgent = fopFactory.newFOUserAgent();
                ByteArrayOutputStream out = new ByteArrayOutputStream();

                Fop fop = fopFactory.newFop(MimeConstants.MIME_PDF, userAgent, out);

                TransformerFactory factory = TransformerFactory.newInstance();
                Transformer transformer = factory.newTransformer(new StreamSource(new File(xslFile)));

                Source src = new StreamSource(new File(xmlFile));
                Result res = new SAXResult(fop.getDefaultHandler());

                transformer.transform(src, res);
                out.close();

                File outputFile = new File(pdfDirectory + "output_" + i + ".pdf");
                FileUtils.writeByteArrayToFile(outputFile, out.toByteArray());
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    });
}

pool.shutdown();
pool.awaitTermination(Long.MAX_VALUE, TimeUnit.NANOSECONDS);