This work reports tunable heterojunction architectures of cobalt oxides (CoOx) nanoparticles confined on well-arrayed graphitic carbon nitride nanotubes (C3N4 NTs) by using a facile one-pot method but under different annealing atmospheres. A Type II heterojunction of cobalt monoxide nanoparticles (CoO NPs)/C3N4 NTs was obtained after annealing under vacuum, and fine CoO NPs less than 8 nm in size were homogeneously anchored on the surface of C3N4 NTs. A Type I heterojunction of tricobalt tetraoxide (Co3O4)/C3N4 NTs were formed under air condition, and Co3O4 NPs in the size range of 20 to 80 nm were aggregated on the surface. The photocatalytic activities of these two heterojunctions were evaluated with hydrogen production from water splitting. The strategically developed CoO/C3N4 NTs with a 7 wt. % CoO shows the highest H-2 yield under visible light irradiation and the best stability among the photocatalysts studied in this work. Comprehensive characterization results reveal that the superior performance of CoO/C3N4 NTs may be attributed to the uniformly distributed smaller nanoparticles on the well-arrayed nanotubes, the longer lifetime of excited electrons, the faster charge transfer and the stronger electronic interaction between the heterojunctions. Our Kelvin probe force microscopy results firmly verify that the CoO/C3N4 NT and Co3O4/C3N4 NT nanocomposites form a Type II and Type I heterojunction, respectively, and charge transfer pathways and reaction mechanisms are therefore established.