Rare and endangered plants (REPs) and their associated endophytes survived in unique habitats are promising sources for natural product-derived drug discovery. In this study, six new (cephaloverines A–F, 1–6, resp.) and 16 known (11–26) cephalotaxine-type alkaloids, together with three new (oliverbiflavones A–C, 7–9, resp.) and 11 known (27–37) biflavonoids were isolated and characterized from the twigs and leaves of Cephalotaxus oliveri, an endangered plant endemic to China. Meanwhile, a preliminary investigation on the secondary metabolites from a selected fungal endophyte (i.e., Alternaria alternate Y-4–2) associated with the title plant led to the isolation of 21 structurally distinct polyketides including one new dimeric xanthone (10). The new structures (1–10) with the absolute configurations were determined by detailed spectroscopic analyses, electronic circular dichroism (ECD) or Na₂MoO₄-induced ECD, the modified Mosher’s method, and some chemical transformations. Compounds 1–4 are the first representatives of naturally occurring N-oxides of cephalotaxine esters, while compounds 7–9 have a special structural feature of having a C-methylated biflavonoid skeleton. The Cephalotaxus alkaloids with ester side-chains at C-3 (1–6, 13–22, and 26) and four biflavonoids (27–29 and 34) were found to show pronounced cytotoxicities against a small panel of human cancer cell lines (A549, NCI-H460, HL60, NCI-H929, and RPMI-8226), with IC₅₀ values mainly ranging from 0.003 to 9.34 μM. The most potent compound, deoxyharringtonine (16), generally exhibited IC₅₀ values less than 10 nM. The structure–activity relationship (SAR) of the aforementioned Cephalotaxus alkaloids was briefly discussed.