The vast and complicated large-qubit state space forbids us to comprehensively capture the dynamics of modern quantum computers via classical simulations or quantum tomography. However, recent progress in quantum learning theory invokes a crucial question: given a quantum circuit containing d tunable RZ gates and G-d Clifford gates, can a learner perform purely classical inference to efficiently predict its linear properties using new classical inputs, after learning from data obtained by incoherently measuring states generated by the same circuit but with different classical inputs? In this work, we prove that the sample complexity scaling linearly in d is necessary and sufficient to achieve a small prediction error, while the corresponding computational complexity may scale exponentially in d. Building upon these derived complexity bounds, we further harness the concept of classical shadow and truncated trigonometric expansion to devise a kernel-based learning model capable of trading off prediction error and computational complexity, transitioning from exponential to polynomial scaling in many practical settings. Our results advance two crucial realms in quantum computation: the exploration of quantum algorithms with practical utilities and learning-based quantum system certification. We conduct numerical simulations to validate our proposals across diverse scenarios, encompassing quantum information processing protocols, Hamiltonian simulation, and variational quantum algorithms up to 60 qubits.