I have a shapefile (my basin limit) and one raster file that I projected it to the shapefile coordinate system and set its cell size to 1000m(area=1Km2). my basin area is 5400 Km2 and it should contain almost 5000 cell of raster file at least. but just one and a half cell put on this range. what's the problem?
As Michael is stating you have gone wrong in the process.
Use the MODIS reprojection tool to output the date in the projection you desire. https://lpdaac.usgs.gov/tools/modis_reprojection_tool
It this statement that is the problem. "it is a modis ET product (MOD 16) and didn't have any coordinate system. my basin projection is Lambert Conformal Conic or UTM-WGS 1984- zone 38N.(both of them is acceptable for my work). so i changed its projection to both of these projection systems but this problem didn't solve. – hadis 9 hours ago"
You cannot just "change" the Projection like this.
Use the tool I showed you and you can set the data to your UTM zone as output.
Then use resample to set the cell size as Michael is saying but the tool does this as well.
You can do it all in ArcGIS but you need to understand the difference between setting a projection and reprojecting. The tool is the way to go.
You should also 100% verify it is the raster that is incorrect (I think it is but am not certain). Sn easy way to do this is bring a base layer in from arcgis (say world imagery) into a fresh MXD then after this add your vector boundaries then after this add your raster and this will confirm which of the two is the problem. Here is the link to the imagery
then get back to us and tell us if it is the raster or vector that is incorrect. I suspect it is the MOD16 and it is an incorrect projection work flow that the tool above fill help resolve.