您可以通过实现自定义装饰器来忽略close。

public class UnClosableDecorator extends InputStream {

    private final InputStream inputStream;

    public UnClosableDecorator(InputStream inputStream) {
        this.inputStream = inputStream;
    }

    @Override
    public int read() throws IOException {
        return inputStream.read();
    }

    @Override
    public int read(byte[] b) throws IOException {
        return inputStream.read(b);
    }

    @Override
    public int read(byte[] b, int off, int len) throws IOException {
        return inputStream.read(b, off, len);
    }

    @Override
    public long skip(long n) throws IOException {
        return inputStream.skip(n);
    }

    @Override
    public int available() throws IOException {
        return inputStream.available();
    }

    @Override
    public synchronized void mark(int readlimit) {
        inputStream.mark(readlimit);
    }

    @Override
    public synchronized void reset() throws IOException {
        inputStream.reset();
    }

    @Override
    public boolean markSupported() {
        return inputStream.markSupported();
    }

    @Override
    public void close() throws IOException {
        //do nothing
    }
}

并在主要使用

public static void main(String[] args) throws Exception {
        System.setIn(new UnClosableDecorator(System.in));
}