We present both a theoretical and a methodological framework that addresses a critical challenge in applying deep learning to physical systems: the reconciliation of non-linear expressiveness with SO(3)-equivariance in predictions of SO(3)-equivariant quantities, such as the electronic-structure Hamiltonian. Inspired by covariant theory in physics, we address this problem by exploring the mathematical relationships between SO(3)-invariant and SO(3)-equivariant quantities and their representations. We first construct theoretical SO(3)-invariant quantities derived from the SO(3)-equivariant regression targets, and use these invariant quantities as supervisory labels to guide the learning of high-quality SO(3)-invariant features. Given that SO(3)-invariance is preserved under non-linear operations, the encoding process for invariant features can extensively utilize non-linear mappings, thereby fully capturing the non-linear patterns inherent in physical systems. Building on this foundation, we propose a gradient-based mechanism to induce SO(3)-equivariant encodings of various degrees from the learned SO(3)-invariant features. This mechanism can incorporate non-linear expressive capabilities into SO(3)-equivariant representations, while theoretically preserving their equivariant properties as we prove. Our approach offers a promising general solution to the critical dilemma between equivariance and non-linear expressiveness in deep learning methodologies. We apply our theory and method to the electronic-structure Hamiltonian prediction tasks, demonstrating state-of-the-art performance across six benchmark databases.