In this study, two types of composite nonwoven fabrics having gradient and inverse gradient of packing density of constituent fabrics were developed and tested for their filtration performance at different operating conditions. These composite nonwoven fabrics were produced by using sequential punching technique by varying the punch densities of the constituent fabrics. Box–Behnken three factors three level design was used, and air velocity, weight of dust fed, and operating time were considered as variables. An instrument for gauging the filtration performance of the composite nonwoven filters was designed and fabricated. The packing density of nonwoven fabrics was measured by using the X-ray computed tomography (XCT) technique. The results depicted those composite nonwoven fabrics having inverse gradient of packing density of constituent fabrics outperformed the composite nonwoven fabrics having gradient of packing density in terms of filtration performance with variable operating conditions.