A nanometer silicon membrane sandwich cup system was self-designed. It could concentrate the bacilli via 0.45-μm microporous filter membrane and semi-automate the acid-fast bacilli (AFB) by a bacteria-staining machine. The aim of the study was to assess the clinical value of our self-designed system for diagnosing tuberculosis (TB). A total of 1993 sputum specimens obtained from patients with confirmed or suspected TB were subjected to direct or concentrated specimens smear at XiangYa Hospital, Central South University between May 2012 and February 2013. In addition, all the specimens were also inoculated into Lowenstein-Jensen (L-J) media, and culture results were considered as the gold standard for calculating sensitivity and specificity. Compared with direct smear examination, an increased density of red stained bacilli was observed in the self-designed nanometer silicon membrane sandwich cup analysis under the microscope. The positive rate of the self-designed analysis was significantly higher than that of direct AFB smear [10.9% (217/1993) vs 6.2% (123/1993), P < 0.05]. The sensitivity of the self-designed system increased (97.3% vs 55.2%, P < 0.05) without a loss of specificity (100% vs 100%) for identifying positive TB cases compared with the direct smear method. The self-designed nanometer silicon membrane sandwich cup and semi-automatic bacteria-staining machine could more efficiently and rapidly detect the AFB in respiratory specimens than direct microscopy. This is a novel and safe examination, and it may replace direct smear examination for the diagnosis of patients with TB.