To further improve the resolution and accuracy of weighing lysimeters, a small-scale local weighing lysimeter system equipped with high-precision weighing sensors and reference buckets which can eliminate the influence of environmental factors on the weighing was developed and then applied to observe rice evapotranspiration (ET) and inter-plant evaporation (E). The results showed that the resolution of ET and E measured by this system can reach 0.005 mm and 0.003 mm, respectively, and the corresponding observation time of peak ET and E are less than a minute (10 s and 20 s for ET and E, respectively) for the identification of the water consumption; moreover, it can still manage 3-5 minutes in the low-throughput phase. The observation accuracy of ET on 15 min, hourly and daily scale by this lysimeter system were improved by 3.51%, 2.17% and 0.77%, and those of E were improved by 18.52%, 11.81% and 2.95%, respectively. It shows that the lysimeter system can produce accurate, stable and reliable data with high resolution, it is applicable to the research of agriculture, hydrology and other related fields, especially for the measurement of small water changes such as short-term evapotranspiration and atmosphere condensed water of ecosystem in arid regions.