Vatsal (Duke Math J 98(2):397-419, 1999) proved that there are congruences between the p-adic L-functions (constructed by Mazur and Swinnerton-Dyer in Invent Math 25:1-61, 1974) of congruent modular forms of the same weight under some conditions. On the other hand, Kim (J Number Theory 144: 188-218, 2014), the second author, constructed two-variable p-adic L-functions of modular forms attached to imaginary quadratic fields generalizing Hida's work (Invent Math 79:159-195, 1985), and the novelty of his construction was that it works whether p is an ordinary prime or not. In this paper, we prove congruences between the two-variable p-adic L-functions (of the second author) of congruent modular forms of different but congruent weights under some conditions when p is a nonordinary prime for the modular forms. This result generalizes the work of Emerton et al. (Invent Math 163(3): 523-580, 2006), who proved similar congruences between the p-adic L-functions of congruent modular forms of congruent weights when p is an ordinary prime.