Thanks for your reply. I followed your steps
diskutil repairDisk disk0
-bash-3.2# diskutil repairDisk disk0
Repairing the partition map might erase disk0s1, proceed? (y/N) y
Started partition map repair on disk0
Checking prerequisites
Checking the partition list
Adjusting partition map to fit whole disk as required
Checking for an EFI system partition
Checking the EFI system partition's size
Checking the EFI system partition's file system
Checking all HFS data partition loader spaces
Checking booter partitions
Checking booter partition disk0s3
Repairing file system
Checking Journaled HFS Plus volume
Checking extents overflow file
Checking catalog file
Checking multi-linked files
Checking catalog hierarchy
Checking extended attributes file
Checking volume bitmap
Checking volume information
The volume Recovery HD appears to be OK
File system check exit code is 0
Updating boot support partitions for the volume as required
Reviewing boot support loaders
Checking Core Storage Physical Volume partitions
Updating Windows boot.ini files as required
The partition map appears to be OK
Finished partition map repair on disk0
Next go to "Reinstall OS X" from the central window
It offers OS X Yosemite 10.10, but can not go through with it.
Then I try booting normally, still not work
Then I Boot the Mac into Single User Mode
fsck -fy
output
/dev/rdisk0s2
Root file system
Executing fsck-hfs(version hfs-285)
checking Journaled HFS Plus Volume
The Volume name is Macintosh HD
Checking extents overflow file
Checking catalog file
pci pause:SDXC
Missing thread record(id=142608777)
Incorrect number of thread records
(4,212637)
Checking multi-linked files
Checking catalog hierarchy
Invalid volume directory count
(It should be 478951 instead of 478952)
Invalid volume file count
(It should be 2184305 instead of 2684306)
Checking extended attributes file
Checking volume bitmap
Volume bitmap needs minor repair for orphaned blocks
Checking volume information
Invalid Volume free block count
(It should be 23236127 instead of 20584173)
Volume header needs minor repair
(2,0)
Repairing volume
Missing directory record(id=142608777)
The volume Macintosh HD could not be repaired
I have tried fsck -fy for five times, it always shows the same