可能不是你日期过滤的问题，在SQL中同时使用and和or，是先执行and，再执行or。不知道你的具体业务逻辑，但是盲猜一下，可能应该需要把or用括号括起来：

WHERE   A.dr = '0' AND (D.code='040102001001' or D.code='040102001002' or D.code='040101001001' or D.code='040101001002' ) 

and 1=1 ${if(len(开始日期)==0,"","and substr(a.dbilldate,1,7) >= '"+开始日期+"'")} 

 ${if(len(结束日期)==0,"","and substr(a.dbilldate,1,7) <= '"+结束日期+"'")} 

如果是字符串的话 你把dbilldate 以及参数中的“-” 取消掉（replace()掉）

${if(len(开始日期)==0,"","and replace(substr(a.dbilldate,1,7),"-","") >= '"+replace(开始日期,"-","")+"'")} 

 ${if(len(结束日期)==0,"","and replace(substr(a.dbilldate,1,7),"-","") <= '"+replace(结束日期,"-","")+"'")} 

SELECT 

          SUBSTR(a.dbilldate,0,4) nianfen, 

          SUBSTR(a.dbilldate,1,7) yuefen,

          (CASE WHEN substr(substr(A.dbilldate, 1, 10), 9, 2) <= 10 THEN

        '上旬' WHEN 11 <= substr(substr(A.dbilldate, 1, 10), 9, 2) AND

        substr(substr(A.dbilldate, 1, 10), 9, 2) <= 20 THEN '中旬'

         WHEN 21 <= substr(substr(A.dbilldate, 1, 10), 9, 2) AND

        substr(substr(A.dbilldate, 1, 10), 9, 2) <= 31 THEN

          '下旬' ELSE  '0'  END) dingdanriq,  

      D.code wljbflbm,

      D.name wlflmc,

      A.nnum  zhusl,

      B.name jldw,

      A.norigtaxmny yuanbijshj,

      A.ntaxmny benbijshj,

      substr(A.dbilldate, 1, 10) riqi

  FROM po_order_b A

  LEFT JOIN bd_measdoc  B

  ON A.cunitid = B.pk_measdoc

  LEFT JOIN bd_material  C

  ON A.pk_srcmaterial =C.pk_material

  LEFT JOIN bd_marbasclass D

  ON C.pk_marbasclass =  D.pk_marbasclass

  LEFT JOIN org_purchaseorg  E

  ON A.pk_org =E.pk_purchaseorg

  WHERE   A.dr = '0' AND D.code='040102001001' or D.code='040102001002' or D.code='040101001001' or D.code='040101001002' 

 and 1=1 ${if(len(开始日期)==0,"","and substr(a.dbilldate,1,7) >= '"+left(开始日期,7)+"'")} 

 ${if(len(结束日期)==0,"","and substr(a.dbilldate,1,7) <= '"+left(结束日期,7)+"'")}