A joint system was proposed to connect square thin‐walled concrete‐filled steel tube (CFST) columns and reinforced concrete (RC) beams. In the system, longitudinal beam reinforcing bars are continuous through the joint zone by passing the rectangular holes in the steel tube, aiming to achieve direct load‐transfer of the beam and joint integrity; and the square thin‐walled steel tube with holes is strengthened by internal diaphragms. Previous cyclic tests showed that the proposed joint system satisfied the requirements of strong‐joint weak‐component, namely the shear capacity of the joint zone was larger than that provided by CFST columns and RC beams. However, further research was necessary to evaluate the behavior under axial compression, as the discontinuous diagonal ribs and holes in the joint steel tube weakened the load capacity. In this investigation, the effect of internal diaphragms was first evaluated based on the axial compression tests on six square CFST stub columns. The test results showed that the internal diaphragms effectively improved the strength and ductility. The finite element analyses (FEA) on square CFST columns and RC beam to CFST column joints stiffened by internal diaphragms were then carried out based on the verified FEA models. The analysis results showed that thicker internal diaphragms increased the strength, and changed the failure mode from the column‐center failure to column‐end failure for columns and from the joint failure to column failure for joints, respectively. Finally, the mechanics‐based models and axial strength equations of square CFST columns and RC beam to CFST column joints stiffened by internal diaphragms were proposed, and the predictions agreed well with the test and analysis results.