Summary: Affine equivalent classes of Boolean functions have many applications in modern cryptography and circuit design. Previous publications have shown that affine equivalence on the entire space of Boolean functions can be computed up to 10 variables, but not on the quotient Boolean function space modulo functions of different degrees. Computing the number of equivalent classes of cosets of Reed-Muller code \(\mathcal{R}(1,n)\) is equivalent to classifying Boolean functions modulo linear functions, which can be computed only when \(n\leq 7\). Based on the linear representation of the affine group \(\mathcal{AGL}(n,2)\) on the quotient space \(\mathcal{R}(s,n)/\mathcal{R}(k,n)\), we obtain a useful counting formula to compute the number of equivalent classes. Instead of computing the conjugacy classes and representatives directly in \(\mathcal{AGL}(n,2)\), we reduce the computation complexity by introducing an isomorphic permutation group \(P_n\) and performing the computation in \(P_n \). With the proposed algorithm, the number of equivalent classes of cosets of \(R(1,n)\) can be computed up to 10 variables. Furthermore, the number of equivalent classes on \(\mathcal{R}(s,n)/\mathcal{R}(k,n)\) can also be computed when \(-1\leq k<s\leq n\leq 10\), which is a major improvement and advancement comparing to previous methods.