This paper presents a mechanism theory principle for equivalent substitution in kinematic chain of a higher pair for lower pairs. This is the opposite of the principle of the equivalent substitution of lower pairs for a higher pair. Also presented here is a new approach for isomorphism identification in kinematic chains containing higher pairs(KCCHs). Based on this approach, an algorithm for generating nonisomorphic KCCHs has been developed. This algorithm is not restricted by the number of links, the degree of freedom or the number of higher pairs. Using this algorithm, nonisomorphic KCCHs can be generated automatically from the kinematic chains that contain only lower pairs. As an application of this algorithm, all the nonisomorphic KCCHs with N < 10(N, the number of links), F ≤3 (F, the degree of KCCHs), and H ≤ 2(H, the number of higher pairs) are computer generated.