您的问题与页边距无关，而是与页脚中的段落设置有关。Word段落设置了每个段落后的行间距以及段落中行间距。如果页脚中的图片在页脚中的段落中是内联的，那么段落后的行间距必须为0，行间距必须为1，以避免您面临的行间距。

使用apache poi 4.1.0可以使用以下方式设置：

...
XWPFParagraph paragraph...
...
paragraph.setSpacingAfter(0);
paragraph.setSpacingBetween(1d, LineSpacingRule.AUTO);
...

完整示例：

import java.io.FileOutputStream;
import java.io.FileInputStream;

import org.apache.poi.xwpf.usermodel.*;
import org.apache.poi.wp.usermodel.HeaderFooterType;
import org.apache.poi.util.Units;

import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTSectPr;
import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTPageSz;
import org.openxmlformats.schemas.wordprocessingml.x2006.main.CTPageMar;

import java.math.BigInteger;

public class CreateWordHeaderFooterNullMargin {

 public static void main(String[] args) throws Exception {

  XWPFDocument document = new XWPFDocument();

  // the body content
  XWPFParagraph paragraph = document.createParagraph();
  XWPFRun run=paragraph.createRun();  
  run.setText("The Body");

  // create header start
  XWPFHeader header = document.createHeader(HeaderFooterType.DEFAULT);
  paragraph = header.getParagraphArray(0);
  if (paragraph == null) paragraph = header.createParagraph();
  paragraph.setSpacingAfter(0);
  paragraph.setSpacingBetween(1d, LineSpacingRule.AUTO);
  run = paragraph.createRun();  
  run.setText("The Header");

  // create footer start
  XWPFFooter footer = document.createFooter(HeaderFooterType.DEFAULT);
  paragraph = footer.getParagraphArray(0);
  if (paragraph == null) paragraph = footer.createParagraph();
  paragraph.setAlignment(ParagraphAlignment.CENTER);
  paragraph.setSpacingAfter(0);
  paragraph.setSpacingBetween(1d, LineSpacingRule.AUTO);
  run = paragraph.createRun();
  String imgFile="Chrysanthemum.jpg";
  run.addPicture(new FileInputStream(imgFile), XWPFDocument.PICTURE_TYPE_JPEG, imgFile, Units.toEMU(500), Units.toEMU(25));

  // create page margins
  CTSectPr sectPr = document.getDocument().getBody().getSectPr();
  if (sectPr == null) sectPr = document.getDocument().getBody().addNewSectPr();
  CTPageSz pageSz = sectPr.addNewPgSz(); // paper format letter
  pageSz.setW(BigInteger.valueOf(12240)); //12240 Twips = 12240/20 = 612 pt = 612/72 = 8.5"
  pageSz.setH(BigInteger.valueOf(15840)); //15840 Twips = 15840/20 = 792 pt = 792/72 = 11"
  CTPageMar pageMar = sectPr.getPgMar();
  if (pageMar == null) pageMar = sectPr.addNewPgMar();
  pageMar.setLeft(BigInteger.valueOf(720)); //720 TWentieths of an Inch Point (Twips) = 720/20 = 36 pt = 36/72 = 0.5"
  pageMar.setRight(BigInteger.valueOf(720));
  pageMar.setTop(BigInteger.valueOf(0));
  pageMar.setBottom(BigInteger.valueOf(0));
  pageMar.setFooter(BigInteger.valueOf(0));
  pageMar.setHeader(BigInteger.valueOf(0));
  pageMar.setGutter(BigInteger.valueOf(0));

  FileOutputStream out = new FileOutputStream("CreateWordHeaderFooterNullMargin.docx");
  document.write(out);
  out.close();
  document.close();

 }
}

免责声明：在我看来，页边距为0的页面设置是不推荐的。大多数打印机无法打印整张纸的大小。纸张的左、右、顶部和/或底部有最小空间的可打印区域。如果您将页边距设置为0，那么Word的GUI将对此发出警告。如果您忽略该警告，那么您可能会在下次打印时损坏打印机。即使您被告知这样做，大多数打印机也不会打印到不可打印的页面范围内。这是为了避免这种损害。