Abstract Electron spins confined in quantum dots are an attractive system to realize high-fidelity qubits owing to their long coherence time. With the prolonged spin coherence time, however, the control fidelity can be limited by systematic errors rather than decoherence, making characterization and suppression of their influence crucial for further improvement. Here we report that the control fidelity of Si/SiGe spin qubits can be limited by the microwave-induced frequency shift of electric dipole spin resonance and it can be improved by optimization of control pulses. As we increase the control microwave amplitude, we observe a shift of the qubit resonance frequency, in addition to the increasing Rabi frequency. We reveal that this limits control fidelity with a conventional amplitude-modulated microwave pulse below 99.8%. In order to achieve a gate fidelity >99.9%, we introduce a quadrature control method, and validate this approach experimentally by randomized benchmarking. Our finding facilitates realization of an ultra-high-fidelity qubit with electron spins in quantum dots.