Abstract We study open-closed orbifold Gromov-Witten invariants of 3-dimensional Calabi-Yau smooth toric Deligne-Mumford stacks (with possibly nontrivial generic stabilisers K and semi-projective coarse moduli spaces) relative to Lagrangian branes of Aganagic-Vafa type. An Aganagic-Vafa brane in this paper is a possibly ineffective $C^\infty $ orbifold that admits a presentation $[(S^1\times \mathbb {R} ^2)/G_\tau ]$ , where $G_\tau $ is a finite abelian group containing K and $G_\tau /K \cong \boldsymbol {\mu }_{\mathfrak {m}}$ is cyclic of some order $\mathfrak {m}\in \mathbb {Z} _{>0}$ . 1. We present foundational materials of enumerative geometry of stable holomorphic maps from bordered orbifold Riemann surfaces to a 3-dimensional Calabi-Yau smooth toric DM stack $\mathcal {X}$ with boundaries mapped into an Aganagic-Vafa brane $\mathcal {L}$ . All genus open-closed Gromov-Witten invariants of $\mathcal {X}$ relative to $\mathcal {L}$ are defined by torus localisation and depend on the choice of a framing $f\in \mathbb {Z} $ of $\mathcal {L}$ . 2. We provide another definition of all genus open-closed Gromov-Witten invariants in (1) based on algebraic relative orbifold Gromov-Witten theory, which agrees with the definition in (1) up to a sign depending on the choice of orientation on moduli of maps in (1). This generalises the definition in [57] for smooth toric Calabi-Yau 3-folds and specifies an orientation on moduli of maps in (1) compatible with the canonical orientation on moduli of relative stable maps determined by the complex structure. 3. When $\mathcal {X}$ is a toric Calabi-Yau 3-orbifold (i.e., when the generic stabiliser K is trivial), so that $G_\tau =\boldsymbol {\mu }_{\mathfrak {m}}$ , we define generating functions $F_{g,h}^{\mathcal {X},(\mathcal {L},f)}$ of open-closed Gromov-Witten invariants of arbitrary genus g and number h of boundary circles; it takes values in $H^*_{ {\mathrm {CR}} }(\mathcal {B} \boldsymbol {\mu }_{\mathfrak {m}}; \mathbb {C} )^{\otimes h}$ , where $H^*_{ {\mathrm {CR}} }(\mathcal {B} \boldsymbol {\mu }_{\mathfrak {m}}; \mathbb {C} )\cong \mathbb {C} ^{\mathfrak {m}}$ is the Chen-Ruan orbifold cohomology of the classifying space $\mathcal {B} \boldsymbol {\mu }_{\mathfrak {m}}$ of $\boldsymbol {\mu }_{\mathfrak {m}}$ . 4. We prove an open mirror theorem that relates the generating function $F_{0,1}^{\mathcal {X},(\mathcal {L},f)}$ of orbifold disk invariants to Abel-Jacobi maps of the mirror curve of $\mathcal {X}$ . This generalises a conjecture by Aganagic-Vafa [6] and Aganagic-Klemm-Vafa [5] (proved in full generality by the first and the second authors in [33]) on the disk potential of a smooth semi-projective toric Calabi-Yau 3-fold.