Although capillary liquid chromatography married with tandem mass spectrometry (cLC-MS/MS) has become a powerful technique for proteomics and metabolomics research, it is still a great challenge to fabricate durable capillary-based analytical columns coupling continuous nanoflow (<1 000 nL/min) electrospray ionization (ESI) with MS, owing to the issue of clogging and fragile of emitters. Here, we proposed a simple approach to integrate microstructured photonic fibers (MPFs) into wide bore capillaries with 150 μm i.d., serving as an integral bifunctional frit or/and ESI emitter of packed columns. Two kinds of MPFs containing 126 homogeneous microchannels with different inner diameter, 3.2 μm for MPF-1 and 2.6 μm for MPF-2, were explored for preparation. The octadecylsilicate (ODS) silica-packed column using MPF-1 as a frit exhibited the lowest plate heights of 14.2-19.7 μm for five alkylbenzenes at the velocity of 1.5 mm/s, which were slightly lower than those of packed column with porous polymer monolith (PPM)-based frit by cLC coupling with ultraviolet (UV) detection. Additionally, the packed columns with integral MPF frit-emitters were further applied in analysis of a complex biological sample of digest of Hela cells by cLC-MS. An average of 7109 unique peptides could be identified in a single analysis by using MPF-1 emitter, and 7110 unique peptides were identified by using the MPF-2 emitter, which were superior to the identified result of packed column with an integral tapered tip emitter (6894 peptides). It is obvious that this novel integral MPF-based frit-emitter does not easily suffer from the issues of cracking owing to the silica cladding around independent microchannels (>100), which always encumbers both independent and integral tapered tip emitters for cLC-MS.