We report the confinement effect induced conformational evolution of one-dimensional (1D) phosphorus atomic chains encapsulated inside carbon nanotubes (CNTs), changing from mono-atomic linear chain to (P8P2)n (n = integer, n ≥ 1) chains as the CNT's inner diameter (diCNT) increases. For a diCNT range of 8.0–10.5 Å, the filled 1D phosphorus appears in monoatomic wide linear chain that possesses an alternative P–P bond configuration with the bond length being 2.0 Å and 2.4 Å respectively, which is a typical behavior of Peierls instability in 1D system. As diCNT increases (indicating weaker confinement), the dominant conformation of the filled phosphorus changes to 1D (P8P2)n (n = integer, n ≥ 1) chains which are consisting of a series of octagons (denoted as P8) and dimers (P2) where the two neighboring octagons are connected with a P2 dimer. Specifically, these encapsulated (P8P2)n chains tend to bend and form helical coils with the helical periodicity increasing with the decreased diCNT as a result of variable confinement effect by the surrounding CNTs. Atomic structures of these 1D phosphorus chains were resolved by high-resolution TEM, image simulation, nanodiffraction, and tilting series imaging. Their chemical information was analyzed via annular dark-field scanning-TEM (ADF-STEM) and STEM-electron energy loss spectroscopy (STEM-EELS) mapping. These CNT inner cavity encapsulated 1D phosphorus chains (monoatomic linear chain and (P8P2)n chain) all exhibited excellent structural stability as demonstrasted by their good resistance to energetic electron beam irradiation. Such a CNT diameter-dependent conformational evolution of 1D phosphorus chains was further quantitatively understood by density-functional theory (DFT) calculations, which also predicted that these 1D phosphorus chains behave semiconducting with direct band gaps and thus they can serve as potential building blocks for nano-electronic and molecular electronic devices.