The primary objective of this study was to determine the relative roles of local environmental (
Local
), geo‐climatic (
Geo
), and spatial (
Spatial
) factors to taxonomic, functional, and phylogenetic
β
‐diversity of stream fish in a large basin in Northeast China. We quantified the current biodiversity patterns of fish communities in the Hun‐Tai River using
β
‐diversity. We assessed (i) corresponding contributions of turnover and nestedness within the taxonomic, functional, and phylogenetic
β
‐diversity of fishes; (ii) correlations among
β
‐diversity facets (i.e., taxonomic, functional, and phylogenetic facets); (iii) relative contributions of
Local
,
Geo
, and
Spatial
factors to
β
‐diversity. We collected fish communities from 171 sampling sites. Mantel tests were used to examine the correlation of three facets of
β
‐diversity and their components (i.e., total, nestedness, and turnover). Distance‐based redundancy analysis and variation partitioning assess the relative contributions of
Local
,
Geo
, and
Spatial
factors to
β
‐diversity. We found that turnover is the main driving mechanism for
β
‐diversity in fish. Among the facets of
β
‐diversity, taxonomic and phylogenetic facets have strong ecological information association.
Spatial
factors have a general contribution to various facets of
β
‐diversity and its components. From aspects of fish
β
‐diversity conservation, connectivity and habitat heterogeneity need to be maintained in the entire aquatic environment. In addition, protecting taxonomic
β
‐diversity is helpful for maintaining phylogenetic
β
‐diversity.