Numerical simulations are usually used to analyze and optimize the performance of the nanofluid-filled absorber tube with fins. However, solving partial differential equations (PDEs) repeatedly requires considerable computational cost. This study develops two deep neural network-based reduced-order models to accurately and rapidly predict the temperature field and heat flux of nanofluid-filled absorber tubes with rectangular fins, respectively. Both network models contain a convolutional path, receiving and extracting cross-sectional geometry information of the absorber tube presented by signed distance function (SDF); then, the following deconvolutional blocks or fully connected layers decode the temperature field or heat flux out from the highly encoded feature map. According to the results, the average accuracy of the temperature field prediction is higher than 99.9% and the computational speed is four orders faster than numerical simulation. For heat flux estimation, the R2 of 81 samples reaches 0.9995 and the average accuracy is higher than 99.7%. The same as the field prediction, the heat flux prediction also takes much less computational time than numerical simulation, with 0.004 s versus 393 s. In addition, the changeable learning rate strategy is applied, and the influence of learning rate and dataset size on the evolution of accuracy are investigated. According to our literature review, this is the first study to estimate the temperature field and heat flux of the outlet cross section in 3D nanofluid-filled fined absorber tubes using a deep convolutional neural network. The results of the current work verify both the high accuracy and efficiency of the proposed network model, which shows its huge potential for the fin-shape design and optimization of nanofluid-filled absorber tubes.