In order for automatic microinjection to serve biomedical and genetic research, we have designed and manufactured a PDMS-based sensor with a circular section channel using the microwire molding technique. For the very precise control of microfluidic transport, we developed a microfluidic pulse width modulation system (MPWM) for automatic microinjections at a picoliter level. By adding a computer-aided detection and tracking of fluid-specific elements in the microfluidic circuit, the PDMS microchannel sensor became the basic element in the automatic control of the microinjection sensor. With the PDMS microinjection sensor, we precise measured microfluidic volumes under visual detection, assisted by very precise computer equipment (with precision below 1 μm) based on image processing. The calibration of the MPWM system was performed to increase the reproducibility of the results and to detect and measure microfluidic volumes. The novel PDMS-based sensor system for MPWM measurements of microfluidic volumes contributes to the advancement of intelligent control methods and techniques, which could lead to new developments in the design, control, and in applications of real-time intelligent sensor system control.