In microchannels, microstructure-induced acoustic streaming can be achieved at low frequencies, providing simple platforms for biomedicine and microfluidic manipulation. Nowadays, microstructures are generally fabricated by photolithography or soft photolithography. Existing studies mainly focused on the projection plane, while ignoring the side profile including microstructure’s sidewall and channel’s upper wall. Based on the perturbation theory, the article focuses on the effect of microstructure’s sidewall errors caused by machining and the viscous dissipation of upper wall on the streaming. We discovered that the side profile parameters, particularly the gap (gap g between the top of the structure and the upper wall of the channel), have a significant impact on the maximum velocity, mode, and effective area of the streaming.To broaden the applicability, we investigated boundary layer thickness parameters including frequency and viscosity. Under different thickness parameters, the effects of side profile parameters on the streaming are similar. But the maximum streaming velocity is proportional to the frequency squared and inversely proportional to the viscosity. Besides, the ratio factor θ of the maximum streaming velocity to the vibration velocity is affected by the side profile parameter gap g and sidewall profile angle α.