Multiscale modeling of complex systems is crucial for understanding their intricacies. Data-driven multiscale modeling has emerged as a promising approach to tackle challenges associated with complex systems. On the other hand, self-similarity is prevalent in complex systems, hinting that large-scale complex systems can be modeled at a reduced cost. In this paper, we introduce a multiscale neural network framework that incorporates self-similarity as prior knowledge, facilitating the modeling of self-similar dynamical systems. For deterministic dynamics, our framework can discern whether the dynamics are self-similar. For uncertain dynamics, it can compare and determine which parameter set is closer to self-similarity. The framework allows us to extract scale-invariant kernels from the dynamics for modeling at any scale. Moreover, our method can identify the power law exponents in self-similar systems. Preliminary tests on the Ising model yielded critical exponents consistent with theoretical expectations, providing valuable insights for addressing critical phase transitions in non-equilibrium systems.