I want to get the information of all genes on human Y chromosome, then I found the statistics in different databases --Ensembl (GENCODE), NCBI, HGNC -- are dissimilar.

For example, protein-coding genes numbers:
	
CCDS	63	
HGNC	45	
Ensembl	63	
NCBI	73	

So what leads to these number be different?

By the way, is RefSeq gene data the same as NCBI homo sapiens annotation release?
The different resources you cite do different things and are not necessarily in sync. The CCDS tries to identify annotations of protein-coding regions in the human and mouse genomes that are consensual across several groups/institutes. The HGNC is in charge of attributing official names and symbols to genes. NCBI's RefSeq is a collection of sequences that are annotated as belonging to a gene and/or linked to other NCBI resources.
Ensembl provides a full genome annotation integrating many information types. Of the resources you cite, Ensembl is the only one that annotates the underlying genome.
When doing a bioinformatics project, select one reference and stick to it. Don't mix and match, this would be asking for trouble. I would recommend using Ensembl because it's much better organized and integrated than NCBI resources.