I have read on website that is B method but I am not sure what is that.
The B-method (or β-method) was introduced by the pioneer work of Baarda, cf. A testing procedure for use in geodetic networks. It describes a procedure to adjust the α-level (type-I error) based on a joint test power (type-II error). JAG3D supports three methods to adjust the significance level. If you don't like to use the B-method, just select your preferred method, cf.
Main menu --> Properties --> Test statistic.
Can you tell me which method is used for deformation analysis and congruence points? Is Karlsruhe, Pelzer...,
The method implemented in JAG3D is described in detail in Kongruenzanalyse auf der Basis originärer Beobachtungen. In contrast to the Karlsruhe or Hannover (Pelzers) approach, which based on preliminary results of (at least) two independent free network adjustments, JAG3D combines the original (raw) observations of both epochs in a joined network adjustment. Like the Karlsruhe approach, JAG3D uses explicit hypothesis tests to detect and to identify possible deformations. From this point of view, it is more related to the Karlsruhe approach.
applied-geodesy.org - OpenSource Least-Squares Adjustment Software for Geodetic Sciences