The miniaturization of analytical systems and the utilization of nontoxic natural extract from plants play significant roles for green analytical chemistry methodology. In this work, the microfluidic hydrodynamic sequential injection (HSI) with the LED-phototransistor colorimetric detection system has been proposed to create an ecofriendly and low-cost miniaturized analytical system for online determination of iron in water samples using Curcuma putii Maknoi & Jenjitt. extracts as high stability and good selectivity of a natural reagent. The proposed method was designed for online solution mixing and colorimetric detection on a microfluidic platform. The Curcuma putii Maknoi & Jenjitt. extracts and standard/samples were sequentially aspirated to fill the channel before entering the built-in flow cell. The intensity of iron-Curcuma putii Maknoi & Jenjitt. extract complex was monitored under the optimum conditions of flow rate, sample volume, mixing zone length, and aspiration sequences, by altering the gain control of the colorimetric detector to achieve good sensitivity. The results demonstrated a good performance of the green analytical systems. A linear calibration graph in the range of 0.5–6.0 mg L−1 was obtained with a limit of detection at an adequate level of 0.11 mg L−1 for water samples with a sample throughput of 30 h−1. The precise and accurate measurement results were achieved with relative standard deviations in the range of 1.61–1.72%, and percent recoveries were found in the range of 90.6–113.4. The proposed method offers cost-effective, easy operation over an appropriate analysis time (2 min/injection) with good sensitivity and is environmentally friendly with low consumption of solutions and the use of high stability and good selectivity of nontoxic reagents. The achieved method was demonstrated to be a good choice for routine analysis.